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Ahmed NA, Gulhan T. Determination of antibiotic resistance patterns and genotypes of Escherichia coli isolated from wild birds. MICROBIOME 2024; 12:8. [PMID: 38191447 PMCID: PMC10773086 DOI: 10.1186/s40168-023-01729-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/21/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND Curbing the potential negative impact of antibiotic resistance, one of our era's growing global public health crises, requires regular monitoring of the resistance situations, including the reservoir of resistance genes. Wild birds, a possible bioindicator of antibiotic resistance, have been suggested to play a role in the dissemination of antibiotic-resistant bacteria. Therefore, this study was conducted with the objective of determining the phenotypic and genotypic antibiotic resistance profiles of 100 Escherichia coli isolates of gull and pigeon origin by using the Kirby-Bauer disk diffusion method and PCR. Furthermore, the genetic relationships of the isolates were determined by RAPD-PCR. RESULTS Phenotypic antibiotic susceptibility testing revealed that 63% (63/100) and 29% (29/100) of E. coli isolates were resistant to at least one antibiotic and multidrug-resistant (MDR), respectively. With the exception of cephalothin, to which the E. coli isolates were 100% susceptible, tetracycline (52%), kanamycin (38%), streptomycin (37%), ampicillin (28%), chloramphenicol (21%), trimethoprim/sulfamethoxazole (19%), gentamicin (13%), enrofloxacin (12%) and ciprofloxacin (12%) resistances were detected at varying degrees. Among the investigated resistance genes, tet(B) (66%), tet(A) (63%), aphA1 (48%), sul3 (34%), sul2 (26%), strA/strB (24%) and sul1 (16%) were detected. Regarding the genetic diversity of the isolates, the RAPD-PCR-based dendrograms divided both pigeon and gull isolates into five different clusters based on a 70% similarity threshold. Dendrogram analysis revealed 47-100% similarities among pigeon-origin strains and 40-100% similarities among gull-origin E.coli strains. CONCLUSIONS This study revealed that gulls and pigeons carry MDR E. coli isolates, which may pose a risk to animal and human health by contaminating the environment with their feces. However, a large-scale epidemiological study investigating the genetic relationship of the strains from a "one health" point of view is warranted to determine the possible transmission patterns of antibiotic-resistant bacteria between wild birds, the environment, humans, and other hosts. Video Abstract.
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Affiliation(s)
- Nejash A Ahmed
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Ondokuz Mayis University, Samsun, Turkey.
- Daro Lebu District Agriculture Office, Mechara-Micheta, Ethiopia.
| | - Timur Gulhan
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Ondokuz Mayis University, Samsun, Turkey
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Zhang S, Shu Y, Wang Y, Zhong Z, Wang M, Jia R, Chen S, Liu M, Zhu D, Zhao X, Wu Y, Yang Q, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Cheng A. High rate of multidrug resistance and integrons in Escherichia coli isolates from diseased ducks in select regions of China. Poult Sci 2023; 102:102956. [PMID: 37586192 PMCID: PMC10450990 DOI: 10.1016/j.psj.2023.102956] [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: 05/20/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 08/18/2023] Open
Abstract
With the increasing number of ducks being raised and consumed, it is crucial to monitor the presence of multidrug resistant (MDR) bacteria in duck farming. Waterfowl, such as ducks, can contribute to the rapid dissemination of antibiotic resistance genes (ARGs). The objective of this study was to investigate the antimicrobial resistance (AMR), ARGs, and mobile genetic elements (MGEs), such as IS26, tbrC, ISEcp1 in Escherichia coli(E. coli) isolated from the intestinal contents of diseased ducks between 2021 and 2022 in Sichuan, Chongqing and Anhui, China. The AMR phenotypes of 201 isolated E. coli strains were determined using the minimum inhibitory concentrations (MICs) method. Subsequently, polymerase chain reaction and sequencing techniques were employed to screen for integron-integrase genes (intI1, intI2, intI3 genes), gene cassettes (GCs), MGEs, and ARGs. The results demonstrated that 96.5% of the E. coli isolates were resistant to at least 1 antibiotic, with 88.1% of the strains displaying MDR phenotype. The highest AMR phenotype observed was for trimethoprim-sulfamethoxazole (88.1%). Furthermore, class 1 and class 2 integrons were detected in 68.2% and 3.0% of all the isolates, respectively, whereas no class 3 integrons were found. Ten types of GCs were identified in the variable regions of class 1 and class 2 integrons. Moreover, 10 MGEs were observed in 46 combinations, with IS26 exhibiting the highest detection rate (89.6%). Among the 22 types of ARGs, tetA (77.1%) was the most frequently detected. In the conjugational transfer experiment, transconjugants were found to carry specific ARGs and MGEs, with their MIC values were significantly higher than those of recipient E. coli J53, indicating their status as MDR bacteria. This study emphasizes the necessity of monitoring MGEs, ARGs, and integrons in duck farms. It provides valuable insights into the complex formation mechanisms of AMR and may aid in preventing and controlling the spread of MDR bacteria in waterfowl breeding farm.
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Affiliation(s)
- Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Yanxi Shu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Yuwei Wang
- Mianyang Academy of Agricultural Sciences, Mianyang, Sichuan 621023, P.R. China
| | - Zhijun Zhong
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Shun Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Mafeng Liu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Xinxin Zhao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Ying Wu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Qiao Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Juan Huang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Xumin Ou
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Sai Mao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Qun Gao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Di Sun
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Bin Tian
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China.
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Saeed MA, Khan AU, Ehtisham-ul-Haque S, Waheed U, Qamar MF, Rehman AU, Nasir A, Zaman MA, Kashif M, Gonzalez JP, El-Adawy H. Detection and Phylogenetic Analysis of Extended-Spectrum β-Lactamase (ESBL)-Genetic Determinants in Gram-Negative Fecal-Microbiota of Wild Birds and Chicken Originated at Trimmu Barrage. Antibiotics (Basel) 2023; 12:1376. [PMID: 37760673 PMCID: PMC10525410 DOI: 10.3390/antibiotics12091376] [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: 07/21/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Extended-spectrum β-lactamases (ESBL) give rise to resistance against penicillin and cephalosporin antibiotics in multiple bacterial species. The present study was conducted to map genetic determinants and related attributes of ESBL-producing bacteria in three wild aquatic bird species and chickens at the "Trimmu Barrage" in district Jhang, Punjab province, Pakistan. To study the prevalence of ESBL-producing bacteria, a total of 280 representative samples were collected from wild bird species; cattle egrets (Bubulcus ibis), little egrets (Egretta garzetta) and common teals (Anas crecca) as well as from indigenous chickens (Gallus gallus domesticus) originating from a local wet market. The isolates were confirmed as ESBL producers using a double disc synergy test (DDST) and bacterial species were identified using API-20E and 20NE strips. A polymerase chain reaction (PCR) was used to detect ESBL genetic determinants and for genus identification via 16S rRNA gene amplification. A phenotypic antimicrobial susceptibility test was performed for ESBL-producing isolates against 12 clinically relevant antibiotics using the Kirby-Bauer disk diffusion susceptibility test. A phylogenetic tree was constructed for the sequence data obtained in this study and comparative sequence data obtained from GenBank. The overall prevalence of ESBL-producing bacteria was 34.64% (97/280). The highest percentage (44.28%; 31/70) of ESBL-producing bacteria was recovered from chickens (Gallus gallus domesticus), followed by little egrets (Egretta garzetta) (41.43%; 29/70), common teal (Anas crecca) (28.57%; 20/70) and cattle egrets (Bubulcus ibis) (24.28%; 17/70). Five different ESBL-producing bacteria were identified biochemically and confirmed via 16S rRNA gene sequencing, which included Escherichia coli (72; 74.23%), Enterobacter cloacae (11; 11.34%), Klebsiella pneumoniae (8; 8.25%), Salmonella enterica (4; 4.12%) and Pseudomonas aeruginosa (2; 2.06%). Based on PCR, the frequency of obtained ESBL genes in 97 isolates was blaCTX-M (51.55%), blaTEM (20.62%), blaOXA (6.18%) and blaSHV (2.06%). In addition, gene combinations blaCTX-M + blaTEM, blaTEM + blaOXA and blaCTX-M + blaSHV were also detected in 16.49%, 2.06% and 1.03% of isolates, respectively. The ESBL gene variation was significant (p = 0.02) in different bacterial species while non-significant in relation to different bird species (p = 0.85). Phylogenetic analysis of amino acid sequence data confirmed the existence of CTX-M-15 and TEM betalactamases. The average susceptibility of the antibiotics panel used was lowest for both Klebsiella pneumoniae (62.5% ± 24.42) and Salmonella enterica (62.5% ± 31.08) as compared to Enterobacter cloacae (65.90% ± 21.62), Pseudomonas aeruginosa (70.83% ± 33.42) and Escherichia coli (73.83% ± 26.19). This study provides insight into the role of aquatic wild birds as reservoirs of ESBL-producing bacteria at Trimmu Barrage, Punjab, Pakistan. Hence, active bio-surveillance and environment preservation actions are necessitated to curb antimicrobial resistance.
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Affiliation(s)
- Muhammad Adnan Saeed
- Department of Pathobiology, University of Veterinary and Animal Sciences, Lahore, CVAS Campus, 12-Km Chiniot Road, Jhang 35200, Pakistan; (A.U.K.); (S.E.-u.-H.); (U.W.); (M.F.Q.); (A.u.R.); (M.A.Z.)
| | - Aman Ullah Khan
- Department of Pathobiology, University of Veterinary and Animal Sciences, Lahore, CVAS Campus, 12-Km Chiniot Road, Jhang 35200, Pakistan; (A.U.K.); (S.E.-u.-H.); (U.W.); (M.F.Q.); (A.u.R.); (M.A.Z.)
| | - Syed Ehtisham-ul-Haque
- Department of Pathobiology, University of Veterinary and Animal Sciences, Lahore, CVAS Campus, 12-Km Chiniot Road, Jhang 35200, Pakistan; (A.U.K.); (S.E.-u.-H.); (U.W.); (M.F.Q.); (A.u.R.); (M.A.Z.)
| | - Usman Waheed
- Department of Pathobiology, University of Veterinary and Animal Sciences, Lahore, CVAS Campus, 12-Km Chiniot Road, Jhang 35200, Pakistan; (A.U.K.); (S.E.-u.-H.); (U.W.); (M.F.Q.); (A.u.R.); (M.A.Z.)
| | - Muhammad Fiaz Qamar
- Department of Pathobiology, University of Veterinary and Animal Sciences, Lahore, CVAS Campus, 12-Km Chiniot Road, Jhang 35200, Pakistan; (A.U.K.); (S.E.-u.-H.); (U.W.); (M.F.Q.); (A.u.R.); (M.A.Z.)
| | - Aziz ur Rehman
- Department of Pathobiology, University of Veterinary and Animal Sciences, Lahore, CVAS Campus, 12-Km Chiniot Road, Jhang 35200, Pakistan; (A.U.K.); (S.E.-u.-H.); (U.W.); (M.F.Q.); (A.u.R.); (M.A.Z.)
| | - Amar Nasir
- Department of Clinical Sciences, University of Veterinary and Animal Sciences, Lahore, CVAS Campus, 12-Km Chiniot Road, Jhang 35200, Pakistan; (A.N.); (M.K.)
| | - Muhammad Arfan Zaman
- Department of Pathobiology, University of Veterinary and Animal Sciences, Lahore, CVAS Campus, 12-Km Chiniot Road, Jhang 35200, Pakistan; (A.U.K.); (S.E.-u.-H.); (U.W.); (M.F.Q.); (A.u.R.); (M.A.Z.)
| | - Muhammad Kashif
- Department of Clinical Sciences, University of Veterinary and Animal Sciences, Lahore, CVAS Campus, 12-Km Chiniot Road, Jhang 35200, Pakistan; (A.N.); (M.K.)
| | - Jean-Paul Gonzalez
- Department of Microbiology & Immunology, School of Medicine, Georgetown University, Washington, DC 20057, USA;
| | - Hosny El-Adawy
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany
- Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh 35516, Egypt
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Ibrahim GA, Salah-Eldein AM, Al-Zaban MI, El-Oksh ASA, Ahmed EM, Farid DS, Saad EM. Monitoring the genetic variation of some Escherichia coli strains in wild birds and cattle. Onderstepoort J Vet Res 2023; 90:e1-e10. [PMID: 37526530 PMCID: PMC10483432 DOI: 10.4102/ojvr.v90i1.2085] [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: 10/13/2022] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 08/02/2023] Open
Abstract
To date, there is limited data about the genetic relationship of Escherichia coli between wild birds and cattle because these birds act as silent vectors for many zoonotic bacteria. This study aimed to elucidate the role of rooming wild birds in the vicinity of cattle farm in transmission of the same pathogenic E. coli variants, identifying their virulence, resistance traits and genetic similarities of fimH virulence gene. About 240 faecal/cloacal swabs were collected from both species and examined bacteriologically. Escherichia coli was yielded in 45.8% and 32.5%, respectively, of examined cattle and wild birds. The most prevalent detected E. coli serovar was O26. High tetracycline and chloramphenicol resistance were recorded; however, gentamycin and ciprofloxacin exhibited the highest sensitivity rates. Polymerase chain reaction (PCR) conserved genotypic resistance (tetA and blaCTX-M) and virulence attributes (fimH, stx1, eaeA and ompA) of E. coli isolates were discussed in detail. The fimH gene revealed 100% sequence similarity when comparing with different E. coli isolates globally and locally. Finally, a close genetic association of E. coli with both wild birds and cattle was detected, thus strengthening its role in the dissemination of the infection via environment. Prevention and conservative policy should be carried as E. coli constitute enormous significant zoonotic risks to livestock and animal workers. Also, further studies to the whole genome sequencing of fimH, other virulence and resistance genes of E. coli are recommended trying to limit the possibilities of co-infection and transfer among different species.Contribution: The current study recorded updated data about the critical infectious role of wild birds to livestock, including cattle farms in Egypt. It also delivered some recommendations for good hygienic practices in cattle farms which must be implemented for handling animal manure.
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Affiliation(s)
- Ghada A Ibrahim
- Bacteriology Department, Agriculture Research Center (ARC), Animal Health Research Institute, Ismailia.
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Gachogo R, Karegi I, Ogoti B, Musyoki V, Martins D, Onyambu F, Kamau J. Draft genome sequences of three emerging beta-lactamase-producing Escherichia coli in the camel production system in Northern Kenya. F1000Res 2023; 11:1413. [PMID: 37654783 PMCID: PMC10466007 DOI: 10.12688/f1000research.127990.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/04/2023] [Indexed: 09/02/2023] Open
Abstract
We report the draft genome sequences and annotation of three beta-lactamase-producing Escherichia coli ( E.coli) strains isolated from fecal samples of healthy camels in Laikipia county, Kenya. This data adds to the online genome resources to support the ongoing antimicrobial resistance surveillance in the livestock-wildlife interface.
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Affiliation(s)
- Rachael Gachogo
- Center for Molecular Biosciences and Genomics, Nairobi, Kenya
- Division of immunology, Department of Human Pathology, University of Cape Town, Cape Town, South Africa
| | - Irene Karegi
- One Health Center, Institute of Primate Research, Nairobi, Kenya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Brian Ogoti
- Center for Microbiology, Washington State University, Nairobi, Kenya
| | - Victor Musyoki
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | | | - Frank Onyambu
- Center for Molecular Biosciences and Genomics, Nairobi, Kenya
- Meru University of Science and Technology, Meru, Kenya
| | - Joseph Kamau
- One Health Center, Institute of Primate Research, Nairobi, Kenya
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Wang X, Zhao J, Ji F, Wang M, Wu B, Qin J, Dong G, Zhao R, Wang C. Genomic Characteristics and Molecular Epidemiology of Multidrug-Resistant Klebsiella pneumoniae Strains Carried by Wild Birds. Microbiol Spectr 2023; 11:e0269122. [PMID: 36840587 PMCID: PMC10101063 DOI: 10.1128/spectrum.02691-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 02/04/2023] [Indexed: 02/24/2023] Open
Abstract
This study aimed to explore the relationship between wild birds and the transmission of multidrug-resistant strains. Klebsiella pneumoniae was isolated from fresh feces of captured wild birds and assessed by the broth microdilution method and comparative genomics. Four Klebsiella pneumoniae isolates showed different resistance phenotypes; S90-2 and S141 were both resistant to ampicillin, cefuroxime, and cefazolin, while M911-1 and S130-1 were sensitive to most of the 14 antibiotics tested. S90-2 belongs to sequence type 629 (ST629), and its genome includes 30 resistance genes, including blaCTX-M-14 and blaSHV-11, while its plasmid pS90-2.3 (IncR) carries qacEdelta1, sul1, and aph(3')-Ib. S141 belongs to ST1662, and its genome includes a total of 27 resistance genes, including blaSHV-217. M911-1 is a new ST, carrying blaSHV-1 and fosA6, and its plasmid pM911-1.1 (novel) carries qnrS1, blaLAP-2, and tet(A). S130-1 belongs to ST3753, carrying blaSHV-11 and fosA6, and its plasmid pS130-1 [IncFIB(K)] carries only one resistance gene, tet(A). pM911-1.1 and pS90-2.3 do not have conjugative transfer ability, but their resistance gene fragments are derived from multiple homologous Enterobacteriaceae strain chromosomes or plasmids, and the formation of resistance gene fragments (multidrug resistance region) involves interactions between multiple mobile element genes, resulting in a complex and diverse resistance plasmid structure. The homologous plasmids related to pM911-1.1 and pS90-2.3 were mainly from isolated human-infecting bacteria in China, namely, K. pneumoniae and Escherichia coli. The multidrug-resistant K. pneumoniae isolates carried by wild birds in this study had drug resistance phenotypes conferred primarily by multidrug resistance plasmids that were closely related to human-infecting bacteria. IMPORTANCE Little is known about the pathogenic microorganisms carried by wild animals. This study found that the multidrug resistance phenotype of Klebsiella pneumoniae isolates carried by wild birds was mainly attributed to multidrug resistance plasmids, and these multidrug resistance plasmids from wild birds were closely related to human-infecting bacteria. Wild bird habitats overlap to a great extent with human and livestock habitats, which further increases the potential for horizontal transfer of multidrug-resistant bacteria among humans, animals, and the environment. Therefore, wild birds, as potential transmission hosts of multidrug-resistant bacteria, should be given attention and monitored.
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Affiliation(s)
- Xue Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Jianan Zhao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Fang Ji
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Meng Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
- College of Veterinary Medicine, Agricultural University of Hebei, Baoding, China
| | - Bin Wu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Jianhua Qin
- College of Veterinary Medicine, Agricultural University of Hebei, Baoding, China
| | - Guoying Dong
- College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Ruili Zhao
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China
| | - Chengmin Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
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Fakorede CO, Amisu KO, Saki M, Akinyemi KO. Co-existence of extended-spectrum β-lactamases bla CTX-M-9 and bla CTX-M-15 genes in Salmonella species isolated from febrile and diarrhoeagenic patients in Lagos, Nigeria: a cross-sectional study. Eur J Med Res 2023; 28:3. [PMID: 36593500 PMCID: PMC9806906 DOI: 10.1186/s40001-022-00960-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/19/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Resistance to different antimicrobial classes by Salmonella species has generated a global public health concern. The spread of extended-spectrum β-lactamases (ESBLs) blaCTX gene variants is also increasing. This study aimed to investigate the antibiotic resistance and the carriage of blaCTX-M-9 and blaCTX-M-15 as well as the quinolone resistance gene (qnrB19) among Salmonella species from hospitalised patients in Lagos, Nigeria. METHODS In this cross-sectional study from April 2021 to August 2021, a total of 508 samples were collected from hospitalised patients. The samples were subjected to standard microbiological investigation. All the isolates were identified using API 20E kits and real-time polymerase chain reaction (RT-PCR). The in vitro antibiotic susceptibility testing (AST) was investigated using the disk diffusion method. Detection of antibiotic resistance and virulence gene makers was conducted using RT-PCR. RESULTS In total, 24 Salmonella species were identified. All the isolates were non-typhoidal Salmonella isolates. None of the isolates screened was S. Typhi and S. Paratyphi. Most of the isolates were susceptible to imipenem, ciprofloxacin, ofloxacin and gentamycin, while a high level of resistance to all cephalosporins, penicillin, and some carbapenems was observed. In total, 79.2% (19/24) of the Salmonella isolates harboured the blaCTX-M variant including 54.2% (13/24) blaCTX-M-9 and 12.5% (3/24) blaCTX-M-15, while co-habitation of blaCTX-M-9 and blaCTX-M-15 was observed in 12.5% (3/24) of the isolates, respectively. None of the isolates harboured quinolone-resistant qnrB19 gene and virulence gene stn. However, invA gene was present in 66.7% (16/24) of all isolates. CONCLUSIONS This study is considered the first report of blaCTX-M-9 and blaCTX-M-15 variants in Salmonella species in Nigeria. The continued existence of cefotaximase (CTX-M)-producing Salmonella within our environment calls for the prudent use of cephalosporins.
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Affiliation(s)
- Christopher O. Fakorede
- grid.411276.70000 0001 0725 8811Department of Microbiology, Faculty of Science, Lagos State University, Lasu Post Office, Ojo, P.O. Box 0001, Lagos, Nigeria
| | - Kehinde O. Amisu
- grid.411276.70000 0001 0725 8811Department of Microbiology, Faculty of Science, Lagos State University, Lasu Post Office, Ojo, P.O. Box 0001, Lagos, Nigeria
| | - Morteza Saki
- grid.411230.50000 0000 9296 6873Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran ,grid.411230.50000 0000 9296 6873Infectious Ophthalmologic Research Center, Imam Khomeini Hospital Clinical Research Development Unit, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Kabiru O. Akinyemi
- grid.411276.70000 0001 0725 8811Department of Microbiology, Faculty of Science, Lagos State University, Lasu Post Office, Ojo, P.O. Box 0001, Lagos, Nigeria
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8
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Muloi DM, Hassell JM, Wee BA, Ward MJ, Bettridge JM, Kivali V, Kiyong'a A, Ndinda C, Gitahi N, Ouko T, Imboma T, Akoko J, Murungi MK, Njoroge SM, Muinde P, Alumasa L, Kaitho T, Amanya F, Ogendo A, van Bunnik BAD, Kiiru J, Robinson TP, Kang'ethe EK, Kariuki S, Pedersen AB, Fèvre EM, Woolhouse MEJ. Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya. BMC Med 2022; 20:471. [PMID: 36482440 PMCID: PMC9730568 DOI: 10.1186/s12916-022-02677-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Livestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here, we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in Escherichia coli, regarded as a sentinel organism. METHODS We conducted a structured epidemiological survey of 99 households across Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311 human, 606 livestock and 399 wildlife faecal samples. We used statistical models to investigate the prevalence of AMR carriage and characterise AMR gene diversity and structure of AMR genes in different host populations across the city. We also investigated household-level risk factors for the exchange of AMR genes between sympatric humans and livestock. RESULTS We detected 56 unique acquired genes along with 13 point mutations present in variable proportions in human and animal isolates, known to confer resistance to nine antibiotic classes. We find that AMR gene community composition is not associated with host species, but AMR genes were frequently co-located, potentially enabling the acquisition and dispersal of multi-drug resistance in a single step. We find that whilst keeping livestock had no influence on human AMR gene carriage, the potential for AMR transmission across human-livestock interfaces is greatest when manure is poorly disposed of and in larger households. CONCLUSIONS Findings of widespread carriage of AMR bacteria in human and animal populations, including in long-distance wildlife species, in community settings highlight the value of evidence-based surveillance to address antimicrobial resistance on a global scale. Our genomic analysis provided an in-depth understanding of AMR determinants at the interfaces of One Health sectors that will inform AMR prevention and control.
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Affiliation(s)
- Dishon M Muloi
- Usher Institute, University of Edinburgh, Edinburgh, UK.
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK.
- International Livestock Research Institute, Nairobi, Kenya.
| | - James M Hassell
- International Livestock Research Institute, Nairobi, Kenya
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
| | - Bryan A Wee
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Melissa J Ward
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Judy M Bettridge
- International Livestock Research Institute, Nairobi, Kenya
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
- Natural Resources Institute, University of Greenwich, Chatham Maritime, UK
| | - Velma Kivali
- International Livestock Research Institute, Nairobi, Kenya
| | - Alice Kiyong'a
- International Livestock Research Institute, Nairobi, Kenya
| | | | | | - Tom Ouko
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - James Akoko
- International Livestock Research Institute, Nairobi, Kenya
| | | | - Samuel M Njoroge
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Patrick Muinde
- International Livestock Research Institute, Nairobi, Kenya
| | - Lorren Alumasa
- International Livestock Research Institute, Nairobi, Kenya
| | - Titus Kaitho
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | | | - Allan Ogendo
- International Livestock Research Institute, Nairobi, Kenya
| | | | - John Kiiru
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Timothy P Robinson
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Rome, Italy
| | | | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Amy B Pedersen
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Eric M Fèvre
- International Livestock Research Institute, Nairobi, Kenya
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
| | - Mark E J Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh, UK.
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK.
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9
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Gulumbe BH, Haruna UA, Almazan J, Ibrahim IH, Faggo AA, Bazata AY. Combating the menace of antimicrobial resistance in Africa: a review on stewardship, surveillance and diagnostic strategies. Biol Proced Online 2022; 24:19. [PMID: 36424530 PMCID: PMC9685880 DOI: 10.1186/s12575-022-00182-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
The emergence of antibiotic-resistant pathogens has threatened not only our ability to deal with common infectious diseases but also the management of life-threatening complications. Antimicrobial resistance (AMR) remains a significant threat in both industrialized and developing countries alike. In Africa, though, poor clinical care, indiscriminate antibiotic use, lack of robust AMR surveillance programs, lack of proper regulations and the burden of communicable diseases are factors aggravating the problem of AMR. In order to effectively address the challenge of AMR, antimicrobial stewardship programs, solid AMR surveillance systems to monitor the trend of resistance, as well as robust, affordable and rapid diagnostic tools which generate data that informs decision-making, have been demonstrated to be effective. However, we have identified a significant knowledge gap in the area of the application of fast and affordable diagnostic tools, surveillance, and stewardship programs in Africa. Therefore, we set out to provide up-to-date information in these areas. We discussed available hospital-based stewardship initiatives in addition to the role of governmental and non-governmental organizations. Finally, we have reviewed the application of various phenotypic and molecular AMR detection tools in both research and routine laboratory settings in Africa, deployment challenges and the efficiency of these methods.
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Affiliation(s)
- Bashar Haruna Gulumbe
- grid.475123.60000 0004 6023 7915Department of Microbiology, Federal University Birnin Kebbi, Kalgo, Kebbi State Nigeria
| | - Usman Abubakar Haruna
- grid.428191.70000 0004 0495 7803Department of Medicine, Nazarbayev University School Medicine, Nursultan, Kazakhstan ,grid.411225.10000 0004 1937 1493Faculty of Pharmaceutical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Joseph Almazan
- grid.428191.70000 0004 0495 7803Department of Medicine, Nazarbayev University School Medicine, Nursultan, Kazakhstan
| | - Ibrahim Haruna Ibrahim
- grid.254145.30000 0001 0083 6092Research Center for Cancer Biology, Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung City, 406040 Taiwan
| | - Abdullahi Adamu Faggo
- grid.449367.b0000 0004 1783 6816Department of Microbiology, Bauchi State University, Gadau, Bauchi State, Nigeria
| | - Abbas Yusuf Bazata
- grid.475123.60000 0004 6023 7915Department of Microbiology, Federal University Birnin Kebbi, Kalgo, Kebbi State Nigeria
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10
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Sun G, Zhang Q, Dong Z, Dong D, Fang H, Wang C, Dong Y, Wu J, Tan X, Zhu P, Wan Y. Antibiotic resistant bacteria: A bibliometric review of literature. Front Public Health 2022; 10:1002015. [PMID: 36466520 PMCID: PMC9713414 DOI: 10.3389/fpubh.2022.1002015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022] Open
Abstract
Antibiotic-resistant bacteria (ARB) are a serious threat to the health of people and the ecological environment. With this problem becoming more and more serious, more countries made research on the ARB, and the research number has been sharply increased particularly over the past decade. Therefore, it is quite necessary to globally retrace relevant researches on the ARB published from 2010 to 2020. This will help researchers to understand the current research situation, research trends and research hotspots in this field. This paper uses bibliometrics to examine publications in the field of ARB from 2010 to 2020 that were retrieved from the Web of Science (WOS). Our study performed a statistical analysis of the countries, institutions, journals, authors, research areas, author keywords, Essential Science Indicators (ESI) highly cited papers, and ESI hotspots papers to provide an overview of the ARB field as well as research trends, research hotspots, and future research directions in the field. The results showed that the number of related studies is increasing year by year; the USA is most published in the field of ARB; China is the most active in this field in the recent years; the Chinese Acad Sci published the most articles; Sci. Total Environ. published the greatest number of articles; CM Manaia has the most contributions; Environmental Sciences and Ecology is the most popular research area; and "antibiotic resistance," "antibiotics," and "antibiotic resistance genes" were the most frequently occurring author keywords. A citation analysis showed that aquatic environment-related antibiotic resistance is a key research area in this field, while antimicrobial nanomaterial-related research is a recent popular topic.
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Affiliation(s)
- Guojun Sun
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Qian Zhang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Zuojun Dong
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Dashun Dong
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Hui Fang
- Institute of Information Resource, Zhejiang University of Technology, Hangzhou, China
| | - Chaojun Wang
- Hangzhou Aeronautical Sanatorium for Special Service of Chinese Air Force, Hangzhou, China
| | - Yichen Dong
- Department of Chinese Medicine, Macau University of Science and Technology, Taipa, Macau SAR, China
| | - Jiezhou Wu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Xuanzhe Tan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Peiyao Zhu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Yuehua Wan
- Institute of Information Resource, Zhejiang University of Technology, Hangzhou, China
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11
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Dreyer S, Globig A, Bachmann L, Schütz AK, Schaufler K, Homeier-Bachmann T. Longitudinal Study on Extended-Spectrum Beta-Lactamase- E. coli in Sentinel Mallard Ducks in an Important Baltic Stop-Over Site for Migratory Ducks in Germany. Microorganisms 2022; 10:1968. [PMID: 36296245 PMCID: PMC9612239 DOI: 10.3390/microorganisms10101968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 08/17/2023] Open
Abstract
Antimicrobial resistance (AMR) is a serious global health threat with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales as the most critical ones. Studies on AMR in wild birds imply a possible dissemination function and indicate their potential role as sentinel animals. This study aimed to gain a deeper insight into the AMR burden of wild waterfowl by sampling semi-wild mallard ducks used as sentinels and to identify if AMR bacteria could be recommended to be added to the pathogens of public health risks to be screened for. In total, 376 cloacal and pooled fecal samples were collected from the sentinel plant over a period of two years. Samples were screened for ESBL-carrying E. coli and isolates found further analyzed using antimicrobial susceptibility testing and whole-genome sequencing. Over the sampling period, 4.26% (16/376) of the samples were positive for ESBL-producing E. coli. BlaCTX-M-1 and blaCTX-M-32 were the most abundant CTX-M types. Although none of the top global sequence types (ST) could be detected, poultry-derived ST115 and non-poultry-related STs were found and could be followed over time. The current study revealed low cases of ESBL-producing E. coli in semi-wild mallard ducks, which proves the suitability of sentinel surveillance for AMR detection in water-associated wildlife.
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Affiliation(s)
- Sylvia Dreyer
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany
| | - Anja Globig
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany
| | - Lisa Bachmann
- Faculty of Agriculture and Food Science, University of Applied Science Neubrandenburg, 17033 Neubrandenburg, Germany
| | - Anne K. Schütz
- Institute of Epidemiology, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
- Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
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12
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Wei X, Wang W, Lu N, Wu L, Dong Z, Li B, Zhou X, Cheng F, Zhou K, Cheng H, Shi H, Zhang J. Prevalence of Multidrug-Resistant CTX-M Extended Spectrum Beta-Lactamase-Producing Escherichia coli From Different Bovine Faeces in China. Front Vet Sci 2022; 9:738904. [PMID: 35978707 PMCID: PMC9376260 DOI: 10.3389/fvets.2022.738904] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 05/19/2022] [Indexed: 01/24/2023] Open
Abstract
CTX-M extended spectrum beta-lactamase-producing Escherichia coli cause severe health hazards in livestock breeding. To date, little is known about antibiotic resistance differences among bacterial isolates from yaks, cows, and beef cattle; therefore, the aims of this study were to analyse the prevalence of CTX-M-producing E. coli in yak, beef cattle, and dairy cattle feces from different provinces in China. A total of 790 fecal samples from yaks, beef cattle, and dairy cows were used. Among all the samples, 523 non duplicate E. coli isolates were identified, and 29.6% of samples harbored CTX-M producers. The results showed that these E. coli strains harbored 15 clusters of CTX-M genes: CTX-M-79, CTX-M-55, CTX-M-15, CTX-M-14, CTX-M-28, CTX-M-179, CTX-M-65, CTX-M-24, CTX-M-27, CTX-M-102, CTX-M-105, CTX-M-173, CTX-M-238, CTX-M-196, and CTX-M-10. The dominant resistance genes were CTX-M-15, CTX-M-14, and CTX-M-55. Moreover, the distribution of CTX-M genes was related to geographical region. Based on the above findings, we reasoned that bovines are potential reservoirs of antibiotic resistance, and this problem should be given adequate attention.
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Affiliation(s)
- Xiaojuan Wei
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Weiwei Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Ningning Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Lingyu Wu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Zhen Dong
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Bing Li
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Xuzheng Zhou
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Fusheng Cheng
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Kairen Zhou
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Haijian Cheng
- Shandong Institute of Animal Science and Veterinary Medicine, Jinan, China
| | - Hongmei Shi
- Gannan Tibetan Autonomous Prefecture Institute of Animal Husbandry Science, Gannan, China
| | - Jiyu Zhang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China,*Correspondence: Jiyu Zhang
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13
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Athanasakopoulou Z, Diezel C, Braun SD, Sofia M, Giannakopoulos A, Monecke S, Gary D, Krähmer D, Chatzopoulos DC, Touloudi A, Birtsas P, Palli M, Georgakopoulos G, Spyrou V, Petinaki E, Ehricht R, Billinis C. Occurrence and Characteristics of ESBL- and Carbapenemase- Producing Escherichia coli from Wild and Feral Birds in Greece. Microorganisms 2022; 10:1217. [PMID: 35744734 PMCID: PMC9227375 DOI: 10.3390/microorganisms10061217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/04/2022] [Accepted: 06/12/2022] [Indexed: 11/16/2022] Open
Abstract
Wild and feral birds are known to be involved in the maintenance and dissemination of clinically-important antimicrobial-resistant pathogens, such as extended-spectrum β-lactamase (ESBL) and carbapenemase-producing Enterobacteriaceae. The aim of our study was to evaluate the presence of ESBL- and carbapenemase-producing Escherichia coli among wild and feral birds from Greece and to describe their antimicrobial resistance characteristics. In this context, fecal samples of 362 birds were collected and cultured. Subsequently, the antimicrobial resistance pheno- and geno-type of all the obtained E. coli isolates were determined. A total of 12 multidrug-resistant (MDR), ESBL-producing E. coli were recovered from eight different wild bird species. Eleven of these isolates carried a blaCTX-M-1 group gene alone or in combination with blaTEM and one carried only blaTEM. AmpC, fluoroquinolone, trimethoprim/sulfamethoxazole, aminoglycoside and macrolide resistance genes were also detected. Additionally, one carbapenemase-producing E. coli was identified, harboring blaNDM along with a combination of additional resistance genes. This report describes the occurrence of ESBL- and carbapenemase-producing E. coli among wild avian species in Greece, emphasizing the importance of incorporating wild birds in the assessment of AMR circulation in non-clinical settings.
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Affiliation(s)
- Zoi Athanasakopoulou
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (A.G.); (A.T.)
| | - Celia Diezel
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (C.D.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07745 Jena, Germany
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (C.D.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07745 Jena, Germany
| | - Marina Sofia
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (A.G.); (A.T.)
| | - Alexios Giannakopoulos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (A.G.); (A.T.)
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (C.D.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07745 Jena, Germany
| | - Dominik Gary
- fzmb GmbH, Forschungszentrum für Medizintechnik und Biotechnologie, 99947 Bad Langensalza, Germany; (D.G.); (D.K.)
| | - Domenique Krähmer
- fzmb GmbH, Forschungszentrum für Medizintechnik und Biotechnologie, 99947 Bad Langensalza, Germany; (D.G.); (D.K.)
| | | | - Antonia Touloudi
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (A.G.); (A.T.)
| | - Periklis Birtsas
- Faculty of Forestry, Wood Science and Design, 43100 Karditsa, Greece;
| | - Matina Palli
- Wildlife Protection & Rehabilitation Center, 24400 Gargalianoi, Greece; (M.P.); (G.G.)
| | | | - Vassiliki Spyrou
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece;
| | | | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (C.D.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07745 Jena, Germany
- Institute of Physical Chemistry, Friedrich-Schiller-University, 07745 Jena, Germany
| | - Charalambos Billinis
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (A.G.); (A.T.)
- Faculty of Public and One Health, University of Thessaly, 43100 Karditsa, Greece;
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14
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Qin J, Zhao Y, Wang A, Chi X, Wen P, Li S, Wu L, Bi S, Xu H. Comparative genomic characterization of multidrug-resistant Citrobacter spp. strains in Fennec fox imported to China. Gut Pathog 2021; 13:59. [PMID: 34645508 PMCID: PMC8513245 DOI: 10.1186/s13099-021-00458-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/06/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND To investigate the antimicrobial profiles and genomic characteristics of MDR-Citrobacter spp. strains isolated from Fennec fox imported from Sudan to China. METHODS Four Citrobacter spp. strains were isolated from stool samples. Individual fresh stool samples were collected and subsequently diluted in phosphate buffered saline as described previously. The diluted fecal samples were plated on MacConkey agar supplemented with 1 mg/l cefotaxime and incubated for 20 h at 37 °C. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) was used for identification. Antimicrobial susceptibility testing was performed using the broth microdilution method. Whole-genome sequencing was performed on an Illumina Novaseq-6000 platform. Acquired antimicrobial resistance genes and plasmid replicons were detected using ResFinder 4.1 and PlasmidFinder 1.3, respectively. Comparative genomic analysis of 277 Citrobacter genomes was also performed. RESULTS Isolate FF141 was identified as Citrobacter cronae while isolate FF371, isolate FF414, and isolate FF423 were identified as Citrobacter braakii. Of these, three C. braakii isolates were further confirmed to be extended-spectrum β-lactamases (ESBL)-producer. All isolates are all multidrug resistance (MDR) with resistance to multiple antimicrobials. Plasmid of pKPC-CAV1321 belong to incompatibility (Inc) group. Comparative genomics analysis of Citrobacter isolates generated a large core-genome. Genetic diversity was observed in our bacterial collection, which clustered into five main clades. Human, environmental and animal Citrobacter isolates were distributed into five clusters. CONCLUSIONS To our knowledge, this is the first investigation of MDR-Citrobacter from Fennec Fox. Our phenotypic and genomic data further underscore the threat of increased ESBL prevalence in wildlife and emphasize that increased effort should be committed to monitoring the potentially rapid dissemination of ESBL-producers with one health perspective.
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Affiliation(s)
- Jie Qin
- Emergency Department of Taizhou Hospital, Taizhou, China
| | - Yishu Zhao
- Department of Rheumatology and Immunology, Shandong Provincial Hospital, Jinan, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Aifang Wang
- Department of Laboratory Medicine, Zhucheng People's Hospital, Zhucheng, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohui Chi
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Peipei Wen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shuang Li
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lingjiao Wu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Sheng Bi
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
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15
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Athanasakopoulou Z, Reinicke M, Diezel C, Sofia M, Chatzopoulos DC, Braun SD, Reissig A, Spyrou V, Monecke S, Ehricht R, Tsilipounidaki K, Giannakopoulos A, Petinaki E, Billinis C. Antimicrobial Resistance Genes in ESBL-Producing Escherichia coli Isolates from Animals in Greece. Antibiotics (Basel) 2021; 10:389. [PMID: 33916633 PMCID: PMC8067336 DOI: 10.3390/antibiotics10040389] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/13/2022] Open
Abstract
The prevalence of multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is increasing worldwide. The present study aimed to provide an overview of the multidrug resistance phenotype and genotype of ESBL-producing Escherichia coli (E. coli) isolates of livestock and wild bird origin in Greece. Nineteen phenotypically confirmed ESBL-producing E. coli strains isolated from fecal samples of cattle (n = 7), pigs (n = 11) and a Eurasian magpie that presented resistance to at least one class of non β-lactam antibiotics, were selected and genotypically characterized. A DNA-microarray based assay was used, which allows the detection of various genes associated with antimicrobial resistance. All isolates harbored blaCTX-M-1/15, while blaTEM was co-detected in 13 of them. The AmpC gene blaMIR was additionally detected in one strain. Resistance genes were also reported for aminoglycosides in all 19 isolates, for quinolones in 6, for sulfonamides in 17, for trimethoprim in 14, and for macrolides in 8. The intI1 and/or tnpISEcp1 genes, associated with mobile genetic elements, were identified in all but two isolates. This report describes the first detection of multidrug resistance genes among ESBL-producing E. coli strains retrieved from feces of cattle, pigs, and a wild bird in Greece, underlining their dissemination in diverse ecosystems and emphasizing the need for a One-Health approach when addressing the issue of antimicrobial resistance.
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Affiliation(s)
- Zoi Athanasakopoulou
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
| | - Martin Reinicke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Celia Diezel
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Marina Sofia
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
| | - Dimitris C. Chatzopoulos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Annett Reissig
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Vassiliki Spyrou
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece;
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institut fuer Medizinische Mikrobiologie und Hygiene, Medizinische Fakultaet “Carl Gustav Carus”, TU Dresden, 01307 Dresden, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07737 Jena, Germany
| | | | - Alexios Giannakopoulos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
| | - Efthymia Petinaki
- Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (K.T.); (E.P.)
| | - Charalambos Billinis
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
- Faculty of Public and Integrated Health, University of Thessaly, 43100 Karditsa, Greece
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