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Tang B, Zhao H, Li J, Liu N, Huang Y, Wang J, Yue M. Detection of clinical Serratia marcescens isolates carrying blaKPC-2 in a hospital in China. Heliyon 2024; 10:e29702. [PMID: 38660286 PMCID: PMC11040119 DOI: 10.1016/j.heliyon.2024.e29702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 04/26/2024] Open
Abstract
Serratia marcescens is an opportunistic and nosocomial pathogen found in the intensive care unit (ICU), but its antimicrobial resistance (AMR) is rarely addressed. Here, we reported two blaKPC-2-positive S. marcescens strains, SMBC31 and SMBC50, recovered from the ICU of a hospital in Zhengzhou, China. The minimum inhibitory concentration (MIC) was determined using the broth microdilution method, while S1-PFGE was employed to demonstrate plasmid size approximation. Complete genome sequences were obtained through Illumina NovaSeq 6000 and Oxford Nanopore Technologies. Both strains exhibit resistance to meropenem and harbor the blaKPC-2 and blaSRT-1 resistance genes. The plasmid pSMBC31-39K in strain SMBC31 and pSMBC50-107K in strain SMBC50 were identified as carrying the blaKPC-2 gene. Notably, both of these plasmids were successfully transferred to Escherichia coli strain J53. Phylogenetic analysis based on plasmid sequences revealed that pSMBC31-39K exhibited high homology with plasmids found in Aeromonas caviae, Citrobacter sp., and Pseudomonas aeruginosa, while pSMBC50-107K showed significant similarity to those of E. coli and Klebsiella pneumoniae. Notably, the coexistence of blaKPC-2 and blaSRT-1 was observed in all 94 KPC-2-producing S. marcescens strains by mining all genomes available under the GenBank database, which were mainly isolated from hospitalized patients. The emergence of multidrug-resistant S. marcescens poses significant challenges in treating clinical infections, highlighting the need for increased surveillance of this pathogen.
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Affiliation(s)
- Biao Tang
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Haoyu Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Jie Li
- College of Life Science, Liaocheng University, Liaocheng, 252000, China
| | - Na Liu
- Translational Medicine Research Center, Fifth Clinical Medical College of Henan University of Chinese Medicine (Zhengzhou People's Hospital), Zhengzhou, 450003, China
| | - Yuting Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Min Yue
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, 310058, China
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Stevens MJA, Stephan R, Horlbog JA, Cernela N, Nüesch-Inderbinen M. Whole genome sequence-based characterization of Campylobacter isolated from broiler carcasses over a three-year period in a big poultry slaughterhouse reveals high genetic diversity and a recurring genomic lineage of Campylobacter jejuni. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 119:105578. [PMID: 38417639 DOI: 10.1016/j.meegid.2024.105578] [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: 01/24/2024] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Campylobacter is among the most frequent agents of bacterial gastroenteritis in Europe and is primarily linked to the consumption of contaminated food. The aim of this study was to assess genomic diversity and to identify antimicrobial resistance and virulence genes of 155 Campylobacter isolated from broiler carcasses (neck skin samples) in a large-scale Swiss poultry abattoir over a three-year period. Samples originated from broilers from three different types of farming systems (particularly animal-friendly stabling (PAFS), free-range farms, and organic farms). Campylobacter jejuni (n = 127) and Campylobacter coli (n = 28) were analysed using a whole genome sequencing (WGS) approach (MiniSeq; Illumina). Sequence types (STs) were determined in silico from the WGS data and isolates were assigned into complex types (CTs) using the cgMLST SeqSphere+ scheme. Antimicrobial resistance genes were identified using the Resistance Gene Identifier (RGI), and virulence genes were identified using the virulence factor database (VFDB). A high degree of genetic diversity was observed. Many sequence types (C. jejuni ST19, ST21, ST48, ST50, ST122, ST262 and C. coli ST827) occurred more than once and were distributed throughout the study period, irrespective of the year of isolation and of the broiler farming type. Antimicrobial resistance determinants included blaOXA and tet(O) genes, as well as the T86I substitution within GyrA. Virulence genes known to play a role in human Campylobacter infection were identified such as the wlaN, cstIII, neuA1, neuB1, and neuC1. Subtyping of the Campylobacter isolates identified the occurrence of a highly clonal population of C. jejuni ST21 that was isolated throughout the three-year study period from carcasses from farms with geographically different locations and different farming systems. The high rate of genetic diversity observed among broiler carcass isolates is consistent with previous studies. The identification of a persisting highly clonal C. jejuni ST21 subtype suggests that the slaughterhouse may represent an environment in which C. jejuni ST21 may survive, however, the ecological reservoir potentially maintaining this clone remains unknown.
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Affiliation(s)
- Marc J A Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
| | - Jule Anna Horlbog
- National Reference Centre for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Magdalena Nüesch-Inderbinen
- National Reference Centre for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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Huang P, Chen C, Zang X, Jiang Q, Lv Y, Lv H, Qin Y, Jiao X, Huang J. The fexA gene in Campylobacter: whether the spread has occurred among various hosts in eastern China. J Glob Antimicrob Resist 2024; 36:293-300. [PMID: 38266959 DOI: 10.1016/j.jgar.2023.12.030] [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: 02/11/2023] [Revised: 08/16/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024] Open
Abstract
OBJECTIVES The emergence of the florfenicol resistance gene fexA in Campylobacter poses a serious threat to public health, but the extent of the spread of fexA in Campylobacter from various hosts has not been well understood. This study aimed to investigate the fexA in Campylobacter isolates from different hosts. METHODS PCR was used to identify fexA-positive Campylobacter from different hosts during 2008-2019 in China, and the fexA-positive isolates were characterized by susceptibility tests, whole-genome sequencing, and natural transformation. RESULTS A total of 69 (2.54%, 69/2721) fexA-positive Campylobacter were identified, and the fexA-positive isolates increased remarkably (0.42%-16.90%) since it was first detected in 2010. By source, the 69 isolates were obtained from chickens (3.57%, 57/1595), geese (3.43%, 7/204), ducks (1.02%, 2/197), and environments (2.86%, 3/105); the fexA-positive isolates were not isolated in humans and pigs. In addition to fexA, these isolates also carried other antimicrobial resistance genes and exhibited multidrug resistance. Whole-genome sequencing analysis showed the fexA gene can disseminate clonally or horizontally via either multidrug resistance genomic islands or insertion sequences among the Campylobacter. The genetic structure IS1216-∆ISEfa11-hp-fexA-NAD(P)H-∆ISEfa11-IS1216 was conserved and widespread in the Campylobacter of various origins, and the IS1216 can form fexA-carrying circular intermediates, emphasizing that IS1216 plays an important role in the spread of fexA in Campylobacter. CONCLUSIONS This study indicates the wide spread of fexA-positive Campylobacter in poultry and environments. Because multidrug resistance genomic islands and IS1216 can facilitate the transmission of fexA, systematic surveillance should be implemented to prevent the spread of fexA to humans.
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Affiliation(s)
- Pingyu Huang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China; Jiangsu Agri-animal Husbandry Vocational College, Taizhou, China
| | - Chong Chen
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Xiaoqi Zang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Qinyue Jiang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yilin Lv
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Hongyue Lv
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yanying Qin
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou, China
| | - Jinlin Huang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou, China.
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Tang B, Siddique A, Jia C, Ed-Dra A, Wu J, Lin H, Yue M. Genome-based risk assessment for foodborne Salmonella enterica from food animals in China: A One Health perspective. Int J Food Microbiol 2023; 390:110120. [PMID: 36758302 DOI: 10.1016/j.ijfoodmicro.2023.110120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 02/06/2023]
Abstract
Salmonella is one of the most common causes of foodborne bacterial disease. Animal-borne foods are considered the primary sources of Salmonella transmission to humans. However, genomic assessment of antimicrobial resistance (AMR) and virulence of Salmonella based on One Health approach remains obscure in China. For this reason, we analyzed the whole genome sequencing data of 134 Salmonella isolates recovered from different animal and meat samples in China. The 134 Salmonella were isolated from 2819 samples (4.75 %) representing various sources (pig, chicken, duck, goose, and meat) from five Chinese provinces (Zhejiang, Guangdong, Jiangxi, Hunan, and Qinghai). AMR was evaluated by the broth dilution method using 13 different antimicrobial agents, and results showed that 85.82 % (115/134) of isolates were resistant to three or more antimicrobial classes and were considered multidrug-resistant (MDR). Twelve sequence types (STs) were detected, with a dominance of ST469 (29.85 %, 40/134). The prediction of virulence genes showed the detection of cdtB gene encoding typhoid toxins in one isolate of S. Muenster recovered from chicken, while virulence genes associated with type III secretion systems were detected in all isolates. Furthermore, plasmid-type prediction showed the abundance of IncFII(S) (13/134; 9.7 %) and IncFIB(S) (12/134; 8.95 %) in the studied isolates. Together, this study demonstrated the ability to use whole-genome sequencing (WGS) as a cost-effective method to provide comprehensive knowledge about foodborne Salmonella isolates in One Health surveillance approach.
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Affiliation(s)
- Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Abubakar Siddique
- Hainan Institute of Zhejiang University, Sanya 572025, China; Atta Ur Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad 44000, Pakistan
| | - Chenhao Jia
- Hainan Institute of Zhejiang University, Sanya 572025, China; Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | | | - Jing Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Hui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Min Yue
- Hainan Institute of Zhejiang University, Sanya 572025, China; Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China.
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Genomic Insights into the Increased Occurrence of Campylobacteriosis Caused by Antimicrobial-Resistant Campylobacter coli. mBio 2022; 13:e0283522. [PMID: 36472434 PMCID: PMC9765411 DOI: 10.1128/mbio.02835-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Campylobacter is the leading bacterial cause of diarrheal illnesses worldwide. Campylobacter jejuni and C. coli are the most common species accounting for campylobacteriosis. Although the proportion of campylobacteriosis caused by C. coli is increasing rapidly in China, the underlying mechanisms of this emergence remain unclear. In this study, we analyzed the whole-genome sequences and associated environments of 1,195 C. coli isolates with human, poultry, or porcine origins from 1980 to 2021. C. coli isolates of human origin were closely related to those from poultry, suggesting that poultry was the main source of C. coli infection in humans. Analysis of antimicrobial resistance determinants indicated that the prevalence of multidrug-resistant C. coli has increased dramatically since the 2010s, coinciding with the shift in abundance from C. jejuni to C. coli in Chinese poultry. Compared with C. jejuni, drug-resistant C. coli strains were better adapted and showed increased proliferation in the poultry production environment, where multiple antimicrobial agents were frequently used. This study provides an empirical basis for the molecular mechanisms that have enabled C. coli to become the dominant Campylobacter species in poultry; we also emphasize the importance of poultry products as sources of campylobacteriosis caused by C. coli in human patients. IMPORTANCE The proportion of campylobacteriosis caused by C. coli is increasing rapidly in China. Coincidentally, the dominant species of Campylobacter occurring in poultry products has shifted from C. jejuni to C. coli. Here, we analyzed the whole-genome sequences of 1,195 C. coli isolates from different origins. The phylogenetic relationship among C. coli isolates suggests that poultry was the main source of C. coli infection in humans. Further analysis indicated that antimicrobial resistance in C. coli strains has increased dramatically since the 2010s, which could facilitate their adaptation in the poultry production environment, where multiple antimicrobial agents are frequently used. Thus, our findings suggest that the judicious use of antimicrobial agents could mitigate the emergence of multidrug-resistant C. coli strains and enhance clinical outcomes by restoring drug sensitivity in Campylobacter.
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Ramamurthy T, Ghosh A, Chowdhury G, Mukhopadhyay AK, Dutta S, Miyoshi SI. Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens. Front Cell Infect Microbiol 2022; 12:952491. [PMID: 36506027 PMCID: PMC9727169 DOI: 10.3389/fcimb.2022.952491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is an important global health problem affecting humans, animals, and the environment. AMR is considered as one of the major components in the "global one health". Misuse/overuse of antibiotics in any one of the segments can impact the integrity of the others. In the presence of antibiotic selective pressure, bacteria tend to develop several defense mechanisms, which include structural changes of the bacterial outer membrane, enzymatic processes, gene upregulation, mutations, adaptive resistance, and biofilm formation. Several components of mobile genetic elements (MGEs) play an important role in the dissemination of AMR. Each one of these components has a specific function that lasts long, irrespective of any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion sequence elements (ISs), and transposons carry the antimicrobial resistance genes (ARGs) on different genetic backbones. Successful transfer of ARGs depends on the class of plasmids, regulons, ISs proximity, and type of recombination systems. Additionally, phage-bacterial networks play a major role in the transmission of ARGs, especially in bacteria from the environment and foods of animal origin. Several other functional attributes of bacteria also get successfully modified to acquire ARGs. These include efflux pumps, toxin-antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling, quorum sensing, two-component system, and clustered regularly interspaced short palindromic repeats (CRISPR) systems. The metabolic and virulence state of bacteria is also associated with a range of genetic and phenotypic resistance mechanisms. In spite of the availability of a considerable information on AMR, the network associations between selection pressures and several of the components mentioned above are poorly understood. Understanding how a pathogen resists and regulates the ARGs in response to antimicrobials can help in controlling the development of resistance. Here, we provide an overview of the importance of genetic network and regulation of AMR in bacterial pathogens.
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Affiliation(s)
- Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India,*Correspondence: Thandavarayan Ramamurthy,
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K. Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-inchi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases at ICMR- National Institute of Cholera and Enteric Diseases, Kolkata, India,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Tang B, Zheng X, Lin J, Wu J, Lin R, Jiang H, Ji X, Yang H, Shen Z, Xia F. Prevalence of the phenicol resistance gene fexA in Campylobacter isolated from the poultry supply chain. Int J Food Microbiol 2022; 381:109912. [PMID: 36081243 DOI: 10.1016/j.ijfoodmicro.2022.109912] [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: 05/10/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 10/31/2022]
Abstract
Florfenicol, an animal-specific broad-spectrum antibiotic, has been widely used in livestock and poultry breeding, which leads to the high antimicrobial resistance (AMR) of Campylobacter in food animals. Recently, a new florfenicol resistance gene, fexA, often located on various multidrug resistance genomic islands (MDRGIs) and confers resistance to various antimicrobial agents, was characterized in Campylobacter. However, the prevalence and genetic environments of fexA and its associated MDRGIs in Campylobacter in the poultry supply chain need further characterization. Here, a total of 111 (15.48 %) Campylobacter isolates (63 C. jejuni, 40 C. coli, 8 C. lari) were obtained from 717 samples from farms, slaughterhouses, and supermarkets. Both phenotypic and genotypic analyses indicated that the AMR of C. coli was significantly higher than that of C. jejuni. PCR amplification and whole genome sequencing showed that the fexA gene was present in 26 out of 35 florfenicol-resistant Campylobacter isolates. This gene was located in the tet(L)-fexA-tet(O) MDRGI. The fexA-harboring isolates detected in the above sources could be clustered into the same branch, indicating that they may have the same ancestor. In addition, the erm(B) gene was identified in 17 Campylobacter isolates, and the A2075G point mutation in the 23S rRNA gene occurred in 26 isolates, emphasizing the high resistance of Campylobacter to macrolides. In summary, these results indicate that fexA within the MDRGI of Campylobacter can be transmitted through bacteria in the animal-based food supply chain, and it is necessary to strengthen the monitoring of the prevalence and spread of fexA in foodborne Campylobacter spp.
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Affiliation(s)
- Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xue Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China; College of Food and Bioengineering, Shaanxi University of Science and Technology, Xian, Shaanxi, China
| | - Jiahui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jing Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Rumeng Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China; Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Han Jiang
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Xiaofeng Ji
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Zhangqi Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory of Food Quality and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Fei Xia
- College of Food and Bioengineering, Shaanxi University of Science and Technology, Xian, Shaanxi, China.
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Quino W, Caro-Castro J, Mestanza O, Hurtado V, Zamudio ML, Cruz-Gonzales G, Gavilan RG. Emergence and Molecular Epidemiology of Campylobacter jejuni ST-2993 Associated with a Large Outbreak of Guillain-Barré Syndrome in Peru. Microbiol Spectr 2022; 10:e0118722. [PMID: 35972275 PMCID: PMC9603473 DOI: 10.1128/spectrum.01187-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/29/2022] [Indexed: 12/30/2022] Open
Abstract
Campylobacter jejuni infection is considered the most frequent factor associated with Guillain-Barré syndrome (GBS). In 2019, a large outbreak of GBS was detected in Peru, being associated with C. jejuni detected in stool samples from these patients. The aim of this study was to determine the molecular epidemiology of C. jejuni strains (ST-2993) associated with a large GBS outbreak in Peru. In this study, 26 C. jejuni strains belonging to the ST-2293, obtained from 2019 to 2020, were sequenced using Illumina technology. Five low-quality sequences were removed using bioinformatics, and 21 genomes (17 clinical strains and 4 chicken strains) were considered in the phylogenetic analysis and comparative genomics. Phylogenetic reconstruction, including genomes from international databases, showed a connection between Peruvian and Chinese GBS strains, both of them having lipooligosaccharides (LOS) locus genes related to molecular mimicry with gangliosides in peripheral nerves. Also, ST-2993 was detected in Amazon strains recovered many years before the 2019 outbreak, but with no epidemiological connection with GBS. Besides, a close relationship between human and chicken C. jejuni strains indicated chicken as one of the probable reservoirs. Finally, comparative genomics revealed differences between Chinese and Peruvian strains, including the presence of a prophage inserted into the genome. In conclusion, C. jejuni ST-2993 strains recovered from the GBS outbreak are closely related to Peruvian Amazon strains. Moreover, ST-2993 has been circulated in Peru since 2003 in the Peruvian Amazonia, showing the necessity to reinforce the epidemiological surveillance of C. jejuni to improve the prevention and control of future GBS outbreaks. IMPORTANCE This article describes the molecular epidemiology of C. jejuni strains (ST-2993) associated with a large Guillain-Barré Syndrome (GBS) outbreak in Peru, sequencing several strains recovered from GBS patients and chickens from 2019 to 2020. Phylogenetic analysis showed a connection between Peruvian and Chinese GBS strains, both of them having lipooligosaccharides (LOS) locus genes related to molecular mimicry with gangliosides in peripheral nerves. Also, ST-2993 strains were detected in isolates recovered many years before the 2019 outbreak, but with no epidemiological connection with GBS. Besides, a close relationship between human and chicken strains indicated those animals as a probable reservoir. This information will help to understand the real situation of GBS in Peru and its causal agent, C. jejuni ST-2993, showing the necessity to increase epidemiological tracking of these kinds of pathogens to detect them and avoid GBS outbreaks in the future.
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Affiliation(s)
- Willi Quino
- Laboratorio de Referencia Nacional de Enteropatógenos, Instituto Nacional de Salud, Lima, Perú
- Escuela Universitaria de Posgrado, Universidad Nacional Federico Villarreal, Lima, Perú
| | - Junior Caro-Castro
- Laboratorio de Referencia Nacional de Enteropatógenos, Instituto Nacional de Salud, Lima, Perú
| | - Orson Mestanza
- Laboratorio de Referencia Nacional de Enteropatógenos, Instituto Nacional de Salud, Lima, Perú
| | - Verónica Hurtado
- Laboratorio de Referencia Nacional de Enteropatógenos, Instituto Nacional de Salud, Lima, Perú
| | - María Luz Zamudio
- Laboratorio de Referencia Nacional de Enteropatógenos, Instituto Nacional de Salud, Lima, Perú
| | - Gloria Cruz-Gonzales
- Escuela Universitaria de Posgrado, Universidad Nacional Federico Villarreal, Lima, Perú
| | - Ronnie G. Gavilan
- Laboratorio de Referencia Nacional de Enteropatógenos, Instituto Nacional de Salud, Lima, Perú
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Perú
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Zhou W, Lin R, Zhou Z, Ma J, Lin H, Zheng X, Wang J, Wu J, Dong Y, Jiang H, Yang H, Yang Z, Tang B, Yue M. Antimicrobial resistance and genomic characterization of Escherichia coli from pigs and chickens in Zhejiang, China. Front Microbiol 2022; 13:1018682. [PMID: 36353453 PMCID: PMC9638057 DOI: 10.3389/fmicb.2022.1018682] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli is considered an opportunistic pathogen and an indicator for antimicrobial resistance (AMR) monitoring. Despite many reports on its AMR monitoring, studies based on genome-based analysis of AMR genes are still insufficient. Here, 181 E. coli strains were isolated from anal swab samples collected from pigs and chickens of animal farms located in Eastern China and sequenced through the Illumina platform. The results showed that 87.85% (159/181) of the E. coli isolates were multidrug-resistant (MDR). Ampicillin (AMP)- spectinomycin (SPT)- tetracycline (TET)- florfenicol (FFC)- sulfisoxazole (SF)- trimethoprim/sulfamethoxazole (SXT) was the predominant AMR pattern. By whole-genome sequencing, we found that ST10 (10.49%, 19/181) and ST48 (7.18%, 13/181) were major sequence types. IncFIB and IncX1 were the most prevalent plasmid replicons. The AMR genes bla NDM-5 (1.10%, 2/181), mcr-1 (1.10%, 2/181), tet(X4) (1.10%, 2/181), and cfr (6.08%, 2/181) were also found in these isolates. In addition, among the 169 virulence genes detected, we identified astA (37.02%, 67/181), hlyA (1.66%, 3/181), hlyB (1.66%, 3/181) and hlyD (1.66%, 3/181), which were closely related to heat-stable enterotoxin 1 and α-hemolysin. In addition, there were 33 virulence genes associated with the iron uptake system, and 46 were adhesion-related genes. Our study highlighted the need for routine surveillance of AMR with advanced genomic approaches, providing up-to-date data on the prevalence of AMR for the development and execution of antimicrobial stewardship policy.
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Affiliation(s)
- Wei Zhou
- Zhejiang Provincial Center for Animal Disease Prevention and Control, Hangzhou, China
| | - Rumeng Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China,School of Food Science and Technology, Jiangnan University, Wuxi, China,Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, China Jiliang University, Hangzhou, China
| | - Zhijin Zhou
- Zhejiang Provincial Center for Animal Disease Prevention and Control, Hangzhou, China
| | - Jiangang Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China,The Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xue Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jingge Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jing Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuzhi Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China,Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, China Jiliang University, Hangzhou, China
| | - Han Jiang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, China Jiliang University, Hangzhou, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhangnv Yang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China,*Correspondence: Zhangnv Yang,
| | - Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China,Biao Tang,
| | - Min Yue
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China,Min Yue,
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10
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Nøhr-Meldgaard K, Struve C, Ingmer H, Agersø Y. Intrinsic tet(L) sub-class in Bacillus velezensis and Bacillus amyloliquefaciens is associated with a reduced susceptibility toward tetracycline. Front Microbiol 2022; 13:966016. [PMID: 35992677 PMCID: PMC9387203 DOI: 10.3389/fmicb.2022.966016] [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: 06/10/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Annotations of non-pathogenic bacterial genomes commonly reveal putative antibiotic resistance genes and the potential risks associated with such genes is challenging to assess. We have examined a putative tetracycline tet(L) gene (conferring low level tetracycline resistance), present in the majority of all publicly available genomes of the industrially important operational group Bacillus amyloliquefaciens including the species B. amyloliquefaciens, Bacillus siamensis and Bacillus velezensis. The aim was to examine the risk of transfer of the putative tet(L) in operational group B. amyloliquefaciens through phylogenetic and genomic position analysis. These analyses furthermore included tet(L) genes encoded by transferable plasmids and other Gram-positive and -negative bacteria, including Bacillus subtilis. Through phylogenetic analysis, we could group chromosomally and plasmid-encoded tet(L) genes into four phylogenetic clades. The chromosomally encoded putative tet(L) from operational group B. amyloliquefaciens formed a separate phylogenetic clade; was positioned in the same genomic region in the three species; was not flanked by mobile genetic elements and was not found in any other bacterial species suggesting that the gene has been present in a common ancestor before species differentiation and is intrinsic. Therefore the gene is not considered a safety concern, and the risk of transfer to and expression of resistance in other non-related species is considered negligible. We suggest a subgrouping of the tet(L) class into four groups (tet(L)1.1, tet(L)1.2 and tet(L)2.1, tet(L)2.2), corresponding with the phylogenetic grouping and tet(L) from operational group B. amyloliquefaciens referred to as tet(L)2.2. Phylogenetic analysis is a useful tool to correctly differentiate between intrinsic and acquired antibiotic resistance genes.
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Affiliation(s)
- Katrine Nøhr-Meldgaard
- Chr. Hansen A/S, Hørsholm, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yvonne Agersø
- Chr. Hansen A/S, Hørsholm, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Yvonne Agersø,
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11
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Jalal K, Khan K, Hayat A, Ahmad D, Alotaibi G, Uddin R, Mashraqi MM, Alzamami A, Aurongzeb M, Basharat Z. Mining therapeutic targets from the antibiotic-resistant Campylobacter coli and virtual screening of natural product inhibitors against its riboflavin synthase. Mol Divers 2022; 27:793-810. [PMID: 35699868 DOI: 10.1007/s11030-022-10455-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/29/2022] [Indexed: 11/29/2022]
Abstract
Campylobacter coli resides in the intestine of several commonly consumed animals, as well as water and soil. It leads to campylobacteriosis when humans eat raw/undercooked meat or come into contact with infected animals. A common manifestation of the infection is fever, nausea, headache, and diarrhea. Increasing antibiotic resistance is being observed in this pathogen. The increased incidence of C. coli infection, and post-infection complications like Guillain-Barré syndrome, make it an important pathogen. It is essential to find novel therapeutic targets and drugs against it, especially with the emergence of antibiotic-resistant strains. In the current study, genomes of 89 antibiotic-resistant strains of C. coli were downloaded from the PATRIC database. Potent drug targets (n = 36) were prioritized from the core genome (n = 1,337 genes) of this species. Riboflavin synthase was selected as a drug target and pharmacophore-based virtual screening was performed to predict its inhibitors from the NPASS (n = ~ 30,000 compounds) natural product library. The top three docked compounds (NPC115144, NPC307895, and NPC470462) were selected for dynamics simulation (for 50 ns) and ADMET profiling. These identified compounds appear safe for targeting this pathogen and can be further validated by experimental analysis before clinical trials.
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Affiliation(s)
- Khurshid Jalal
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Ajmal Hayat
- Department of Pharmacy, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Diyar Ahmad
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Ghallab Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Al-Dawadmi Campus, Shaqra University, Shaqra, Saudi Arabia
| | - Reaz Uddin
- Computational Biology Unit, Lab 103 PCMD ext. Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, 61441, Saudi Arabia
| | - Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Science, Shaqra University, AlQuwayiyah, 11961, Saudi Arabia
| | - Muhammad Aurongzeb
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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12
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Antimicrobial resistance in Campylobacter coli and Campylobacter jejuni from human campylobacteriosis in Taiwan, 2016-2019. Antimicrob Agents Chemother 2021; 66:e0173621. [PMID: 34748382 DOI: 10.1128/aac.01736-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Campylobacter coli and C. jejuni are highly resistant to most therapeutic antimicrobials in Taiwan, rapid diagnostics of resistance in bacterial isolates is crucial for the treatment of campylobacteriosis. We characterized 219 (40 C. coli and 179 C. jejuni) isolates recovered from humans between 2016 and 2019 using whole-genome sequencing to investigate the genetic diversity among isolates and the genetic resistance determinants associated with antimicrobial resistance. Susceptibility testing with 8 antimicrobials was conducted to assess the concordance between phenotypic resistance and genetic determinants. The conventional and core genome multilocus sequence typing analysis revealed diverse clonality among the isolates. Mutations in gyrA (T86I, D90N), rpsL (K43R, K88R), and 23S rRNA (A2075G) were found in 91.8%, 3.2%, and 6.4% of the isolates, respectively. Horizontally transferable resistance genes ant(6)-I, aad9, aph(3')-IIIa, aph(2"), blaOXA, catA/fexA, cfr(C), erm(B), lnu, sat4, and tet were identified in 24.2%, 21.5%, 33.3%, 11.9%, 96.3%, 10.0%, 0.9%, 6.8%, 3.2%, 13.2%, and 96.3%, respectively. High-level resistance to 8 antimicrobials in isolates was 100% predictable by the known resistance determinants, whereas low-level resistance to azithromycin, clindamycin, nalidixic acid, ciprofloxacin, and florfenicol in isolates was associated with sequence variations in CmeA and CmeB of the CmeABC efflux pump. Resistance-enhancing CmeB variants were identified in 62.1% (136/219) of isolates. In conclusion, an extremely high proportion of C. coli (100%) and C. jejuni (88.3%) were multidrug-resistant and a high proportion (62.5%) of C. coli isolates had been resistant to azithromycin, erythromycin, and clindamycin that would complicate the treatment of invasive campylobacteriosis in this country.
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13
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson‐Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López‐Alonso M, Nielsen SS, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Innocenti ML, Liébana E, López‐Gálvez G, Manini P, Stella P, Peixe L. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 7: Amphenicols: florfenicol and thiamphenicol. EFSA J 2021; 19:e06859. [PMID: 34729087 PMCID: PMC8546524 DOI: 10.2903/j.efsa.2021.6859] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The specific concentrations of florfenicol and thiamphenicol in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield, were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for florfenicol was estimated. However, due to the lack of data, the calculation of the FARSC for thiamphenicol was not possible until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for florfenicol, whilst for thiamphenicol no suitable data for the assessment were available. Uncertainties and data gaps associated to the levels reported were addressed. For florfenicol, it was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC, whereas for thiamphenicol, the recommendation was to generate the data required to fill the gaps which prevented the FARSC calculation.
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14
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Ma L, Konkel ME, Lu X. Antimicrobial Resistance Gene Transfer from Campylobacter jejuni in Mono- and Dual-Species Biofilms. Appl Environ Microbiol 2021; 87:e0065921. [PMID: 33990313 PMCID: PMC8276811 DOI: 10.1128/aem.00659-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/13/2021] [Indexed: 01/16/2023] Open
Abstract
Horizontal gene transfer (HGT) is a driving force for the dissemination of antimicrobial resistance (AMR) genes among Campylobacter jejuni organisms, a leading cause of foodborne gastroenteritis worldwide. Although HGT is well documented for C. jejuni planktonic cells, the role of C. jejuni biofilms in AMR spread that likely occurs in the environment is poorly understood. Here, we developed a cocultivation model to investigate the HGT of chromosomally encoded AMR genes between two C. jejuni F38011 AMR mutants in biofilms. Compared to planktonic cells, C. jejuni biofilms significantly promoted HGT (P < 0.05), resulting in an increase of HGT frequencies by up to 17.5-fold. Dynamic study revealed that HGT in biofilms increased at the early stage (i.e., from 24 h to 48 h) and remained stable during 48 to 72 h. Biofilms continuously released the HGT mutants into supernatant culture, indicating spontaneous dissemination of AMR to broader niches. DNase I treatment confirmed the role of natural transformation in genetic exchange. HGT was not associated with biofilm biomass, cell density, or bacterial metabolic activity, whereas the presence of extracellular DNA was negatively correlated with the altered HGT frequencies. HGT in biofilms also had a strain-to-strain variation. A synergistic HGT effect was observed between C. jejuni with different genomic backgrounds (i.e., C. jejuni NCTC 11168 chloramphenicol-resistant strain and F38011 kanamycin-resistant strain). C. jejuni performed HGT at the frequency of 10-7 in Escherichia coli-C. jejuni biofilms, while HGT was not detectable in Salmonella enterica-C. jejuni biofilms. IMPORTANCE Antimicrobial-resistant C. jejuni has been listed as a high priority of public health concern worldwide. To tackle the rapid evolution of AMR in C. jejuni, it is of great importance to understand the extent and characteristics of HGT in C. jejuni biofilms, which serve as the main survival strategy of this microbe in the farm-to-table continuum. In this study, we demonstrated that biofilms significantly enhanced HGT compared to the planktonic state (P < 0.05). Biofilm cultivation time and extracellular DNA (eDNA) amount were related to varied HGT frequencies. C. jejuni could spread AMR genes in both monospecies and dual-species biofilms, mimicking the survival mode of C. jejuni in food chains. These findings indicated that the risk and extent of AMR transmission among C. jejuni organisms have been underestimated, as previous HGT studies mainly focused on the planktonic state. Future AMR controlling measures can target biofilms and their main component eDNA.
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Affiliation(s)
- Luyao Ma
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael E. Konkel
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Quebec, Canada
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15
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Abstract
Florfenicol is widely used for the treatment of respiratory infections and as a feed additive in food animal production. As a foodborne pathogen, Campylobacter is constantly exposed to florfenicol, and resistance to this antimicrobial agent has increased in recent years. Previous studies indicated that Campylobacter has developed several mechanisms that confer resistance to florfenicol, which is used in food animal production. This study describes the coexistence of optrA and fexA in Campylobacter jejuni and Campylobacter coli isolates from pigs and poultry. Moreover, whole-genome sequencing data showed that the two genes are located in various multidrug resistance genomic islands within different regions of the Campylobacter genomes. The emergence of optrA and fexA may support the spread of florfenicol-resistant Campylobacter strains of animal origin. IMPORTANCE Florfenicol is widely used for the treatment of respiratory infections and as a feed additive in food animal production. As a foodborne pathogen, Campylobacter is constantly exposed to florfenicol, and resistance to this antimicrobial agent has increased in recent years. Previous studies indicated that Campylobacter has developed several mechanisms that confer resistance to florfenicol. This study describes for the first time the coexistence of the florfenicol exporter FexA and the ribosomal protective protein OptrA in Campylobacter jejuni isolated from pigs. The two genes were located in various multidrug resistance genomic islands within different regions of the Campylobacter genomes. Although phenicols are not commonly used for the treatment of Campylobacter infections, the extensive use of florfenicol in food animals may play a role in the coselection of multidrug resistance genomic island (MDRGI)-carrying Campylobacter isolates which also exhibited resistance to critically important antimicrobial agents (macrolides, aminoglycosides, and tetracyclines) commonly used for the treatment of human campylobacteriosis.
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Emergence of a Novel tet(L) Variant in Campylobacter spp. of Chicken Origin in China. Antimicrob Agents Chemother 2020; 65:AAC.01622-20. [PMID: 33046498 DOI: 10.1128/aac.01622-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/06/2020] [Indexed: 12/30/2022] Open
Abstract
Tetracyclines are widely used in veterinary medicine and food animal production. Campylobacter members are major foodborne pathogens, and their resistance to tetracycline has been widely reported in different countries. To date, Tet(O), a ribosomal protection protein, is the only confirmed Tet resistance determinant in Campylobacter spp. Here, we reported the detection and characterization of a novel Tet resistance element in Campylobacter spp. of chicken origin. This gene is identified to be a variant of tet(L), which encodes an efflux pump for Tet resistance. The variant was detected in 14 of the 82 tetracycline-resistant Campylobacter isolates collected from chickens in Henan, China. Cloning of the tet(L) variant into tetracycline-susceptible Campylobacter jejuni NCTC 11168 confirmed its function in conferring resistance to tetracycline and doxycycline. In addition, this tet(L) variant elevated the MIC (4-fold increase) of tigecycline in the heterologous Escherichia coli host. Sequencing analysis indicated the tet(L) variant was located within a multidrug-resistance genomic island (MDRGI) containing tet(L) variant IS1216E-ORF1-fexA-Δtnp-IS1216E-tet(O)-tnpV-repA This MDRGI is inserted into conserved gene potB on the chromosome. Multilocus sequence type (MLST) analysis revealed that both clonal expansion and horizontal transfer were involved in the dissemination of the tet(L) variant. These findings reveal the emergence of a new Tet resistance determinant in Campylobacter spp., which may facilitate their adaptation to the antimicrobial selection pressure in chickens.
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Tang Y, Lai Y, Wang X, Lei C, Li C, Kong L, Wang Y, Wang H. Novel insertion sequence ISChh1-like mediating acquisition of optrA gene in foodborne pathogen Campylobacter coli of swine origin. Vet Microbiol 2020; 252:108934. [PMID: 33249367 DOI: 10.1016/j.vetmic.2020.108934] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
The optrA gene encodes an ABC-F protein which confers cross-resistance to oxazolidinones and phenicols, and its transmission has so far been associated with multiple transposable elements, including IS1216E, prophages, ICEs and Tn558. Here, we identified an optrA gene flanked by two copies of a novel insertion sequence ISChh1-like in the same direction in Campylobacter coli. Seven optrA-positive C. coli were identified from 263 Campylobacter isolates obtained from one swine farm and two slaughterhouses in Sichuan province of China. The optrA genes in 6 isolates were directly flanked by two copies of ISChh1-like elements in the same orientation, in the remaining one isolate, optrA was co-located with fexA and flanked by two copies of IS1216E and inserted in the downstream of the aadE-sat4-aphA3 gene cluster on chromosome. Cloning of optrA into C. jejuni NCTC 11,168 confirmed its role in elevated MICs to oxazolidinones and phenicols. Translocatable units (TUs) and natural transformants were only detected from the isolate with optrA bracketed by IS1216E, not from these with optrA bracketed by ISChh1-like. ISChh1-like in all isolates inserts specifically either next to or between adjacent GG nucleotides, neither have terminal inverted repeats nor generate target site duplications. Interestingly, ISChh1-like were also found mediating integration of other antibiotic resistance genes in Campylobacter, including tet(O), aphA3 and aadE-sat4-aphA3 gene cluster. Taken together, these results identify ISChh1-like as a novel transposon mediating acquisition of multiple antibiotic resistance genes in Campylobacter, including the very important optrA gene, suggesting that it plays an essential role in the transmission of antibiotic resistance genes to Campylobacter.
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Affiliation(s)
- Yizhi Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Yan Lai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Xingyuan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Changwei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Chao Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Linghan Kong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Yulong Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China.
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Genetic environments and related transposable elements of novel cfr(C) variants in Campylobacter coli isolates of swine origin. Vet Microbiol 2020; 247:108792. [DOI: 10.1016/j.vetmic.2020.108792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 01/05/2023]
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