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Zaidi SEZ, Zaheer R, Zovoilis A, McAllister TA. Enterococci as a One Health indicator of antimicrobial resistance. Can J Microbiol 2024; 70:303-335. [PMID: 38696839 DOI: 10.1139/cjm-2024-0024] [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] [Indexed: 05/04/2024]
Abstract
The rapid increase of antimicrobial-resistant bacteria in humans and livestock is concerning. Antimicrobials are essential for the treatment of disease in modern day medicine, and their misuse in humans and food animals has contributed to an increase in the prevalence of antimicrobial-resistant bacteria. Globally, antimicrobial resistance is recognized as a One Health problem affecting humans, animals, and environment. Enterococcal species are Gram-positive bacteria that are widely distributed in nature. Their occurrence, prevalence, and persistence across the One Health continuum make them an ideal candidate to study antimicrobial resistance from a One Health perspective. The objective of this review was to summarize the role of enterococci as an indicator of antimicrobial resistance across One Health sectors. We also briefly address the prevalence of enterococci in human, animal, and environmental settings. In addition, a 16S RNA gene-based phylogenetic tree was constructed to visualize the evolutionary relationship among enterococcal species and whether they segregate based on host environment. We also review the genomic basis of antimicrobial resistance in enterococcal species across the One Health continuum.
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Affiliation(s)
- Sani-E-Zehra Zaidi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- University of Manitoba, Department of Biochemistry and Medical Genetics, 745 Bannatyne Ave, Winnipeg
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- University of Manitoba, Department of Biochemistry and Medical Genetics, 745 Bannatyne Ave, Winnipeg
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
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Chen W, Wang Q, Wu H, Xia P, Tian R, Li R, Xia L. Molecular epidemiology, phenotypic and genomic characterization of antibiotic-resistant enterococcal isolates from diverse farm animals in Xinjiang, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168683. [PMID: 37996027 DOI: 10.1016/j.scitotenv.2023.168683] [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: 06/11/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Multidrug-resistant (MDR) bacteria in farm environments can be transferred to humans through the food chain and occupational exposure. Enterococcus infections caused by linezolid resistant enterococci (LRE) are becoming more challenging to treat as their resistance to antibiotics intensifies. Therefore, this study investigated the molecular epidemiology, phenotypic and genomic characterization of enterococci in seven species of farm animals (sheep, chicken, swine, camel, cattle, equine, pigeon) anal swab from Xinjiang, China by agar dilution method, polymerase chain reaction (PCR), whole-genome sequencing (WGS) and bioinformatics analysis. A total of 771 samples were collected, 599 (78 %) were contaminated with Enterococcus spp., among which Enterococcus faecalis (350/599) was dominant. Antimicrobial susceptibility testing showed that high resistance was observed in rifampicin (80 %), tetracycline (71 %), doxycycline (71 %), and erythromycin (69 %). The results of PCR showed the highest prevalent antibiotic resistance genes (ARGs) were aac(6')-aph(2″) (85 %), followed by tet(M) (73 %), erm(B) (62 %), and aph(3')-IIIa (61 %). Besides, 29 optrA-carrying E. faecalis isolates belonging to 13 STs (including 3 new alleles) were detected, with ST714 (31 %, 9/29) being the dominant ST type. The phylogenetic tree showed that optrA-carrying E. faecalis prevalent in the intensive swine farm is mainly caused by clonal transmission. Notably, optrA gene in Enterococcus spp. isolate from camel was first characterized here. WGS of E. faecalis F109 isolate from camel confirmed the colocalization of optrA with other five ARGs in the same plasmid (pAFL-109F). The optrA-harboring genetic context is IS1216E-fexA-optrA-erm(A)-IS1216E. This study highlights the prevalence of MDR Enterococcus (≥88 %) and four ARGs (≥75 %) in swine (intensive farming), cattle (commercial farming), and chickens (backyard farming) are high and also highlights that optrA-carrying E. faecalis of farm animals incur a transmission risk to humans through environment, food consumption and others. Therefore, antibiotic-resistant bacteria (ARB) monitoring and effective control measures should be strengthened and implemented in diverse animals.
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Affiliation(s)
- Wanzhao Chen
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China; Xinjiang Key Laboratory of Herbivore Drug Research and Creation, Xinjiang Agricultural University, Urumqi 830052, China
| | - Qiaojun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Huimin Wu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Panpan Xia
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Rui Tian
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.
| | - Lining Xia
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China; Xinjiang Key Laboratory of Herbivore Drug Research and Creation, Xinjiang Agricultural University, Urumqi 830052, China.
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Wang Q, Peng K, Liu Z, Li Y, Xiao X, Du XD, Li R, Wang Z. Genomic insights into linezolid-resistant Enterococci revealed its evolutionary diversity and poxtA copy number heterogeneity. Int J Antimicrob Agents 2023; 62:106929. [PMID: 37487950 DOI: 10.1016/j.ijantimicag.2023.106929] [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: 04/12/2023] [Revised: 07/03/2023] [Accepted: 07/15/2023] [Indexed: 07/26/2023]
Abstract
OBJECTIVES This study aimed to determine the molecular mechanisms of linezolid-resistant enterococci (LRE) in swine slaughterhouses in China and apply the "One Health" perspective to analyse the evolutionary dynamics of poxtA-positive E. faecium in clinical and non-clinical settings worldwide. METHODS The phenotypic and genomic characteristics of multiple LRE isolates were systematically investigated using antimicrobial susceptibility testing, transfer assays, evolutionary experiments, quantitative RT-PCR assays, whole-genome sequencing, and bioinformatics analyses. RESULTS Swine faeces served as a significant reservoir for LRE isolates, and optrA and poxtA were the primary contributors to linezolid resistance. Co-occurrence network analysis revealed a significant interconnection between optrA and several other ARGs. The poxtA copy number heterogeneity and polymorphism were initially observed in E. faecium parental and evolved isolates. The poxtA-carrying tandem repeat region exhibits high mobility and has undergone extensive duplication owing to linezolid pressure. The poxtA copy number varies from four copies on the plasmid of E. faecium IC25 to 11 copies on the plasmid and six copies on the chromosome in the evolved isolate IC25-50_poxtA. Furthermore, phylogenetic analysis of 185 poxtA-positive E. faecium strains worldwide found that one isolate from a French patient in 2018 shared only two SNPs with CC17 E. faecium isolates IC25 and IC7-2 from this study, highlighting the potential global transmission of CC17 poxtA-positive E. faecium between humans and animals. CONCLUSION This study identified amplification of poxtA as a response of E. faecium to linezolid pressure. Phylogenetic analysis shed light on the potential global transmission of hospital-associated CC17 poxtA-positive E. faecium in clinical and non-clinical settings.
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Affiliation(s)
- Qiaojun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Ziyi Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Yan Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Xia Xiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, P. R. China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China.
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P. R. China.
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Torabi M, Faghri J, Poursina F. Detection of Genes Related to Linezolid Resistance ( poxtA, cfr, and optrA) in Clinical Isolates of Enterococcus spp. from Humans: A First Report from Iran. Adv Biomed Res 2023; 12:205. [PMID: 37694234 PMCID: PMC10492618 DOI: 10.4103/abr.abr_74_23] [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: 02/25/2023] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 09/12/2023] Open
Abstract
Background Enterococci may develop resistance to linezolid through chromosomal mutations that involve specific linezolid resistance genes, such as cfr, optrA, and poxtA. The objective of this study was to evaluate the antibiotic susceptibility of enterococcal isolates and identify cfr, optrA, and poxtA genes in MDR isolates. Materials and Methods Enterococcal isolates were collected from various clinical specimens at Al-Zahra, Amin, and Khorshid Hospitals in Isfahan. The Enterococcus isolates were identified as belonging to the E. faecalis and E. faecium species by using specific gene (D alanine D alanine ligase ddl) sets in PCR. To detect cfr, optrA, and poxtA genes among the species, a multiplex-PCR assay was performed. Results Out of 175 isolates, E. faecalis predominated 129/175 (73.7%). Furthermore, the prevalence of vancomycin-resistant Enterococci (VRE) and linezolid-resistant Enterococci (LRE) was 29.7% and 4%, respectively. The overall prevalence of MDR was 91.1%, 68.9%, and 66.6% of E. faecium, E. faecalis, and other Enterococcus spp., respectively. Interestingly, the frequency of optrA (71.4%) in E. faecium and poxtA and crf (42.8%) in E. faecalis were detected among LRE species. A statistically significant relationship (P < 0.05) was found between the presence of the three genes and the occurrence of LRE. Conclusion This is the first study to report the detection of linezolid resistance genes (cfr, optrA, and poxtA) in clinical Enterococcus spp. isolates from Iran, conducted at Isfahan University of Medical Sciences hospitals. The emergence of enterococcal strains that resist linezolid is concerning as it can lead to the spread of resistant strains among patients, resulting in treatment failure.
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Affiliation(s)
- Majid Torabi
- Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jamshid Faghri
- Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farkhondeh Poursina
- Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Li XS, Qi Y, Li PH, Xue JZ, Li XY, Muhammad I, Li YZ, Zhu DM, Ma Y, Kong LC, Ma HX. Genetic characterization of MDR genomic elements carrying two aac(6')- aph(2″) genes in feline-derived clinical Enterococcus faecalis isolate. Front Microbiol 2023; 14:1191837. [PMID: 37577435 PMCID: PMC10413266 DOI: 10.3389/fmicb.2023.1191837] [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: 03/22/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Multidrug-resistant Enterococcus faecalis (E. faecalis) often cause intestinal infections in cats. The aim of this study was to investigate a multidrug-resistant E. faecalis isolate for plasmidic and chromosomal antimicrobial resistance and their genetic environment. E. faecalis strain ESC1 was obtained from the feces of a cat. Antimicrobial susceptibility testing was carried out using the broth microdilution method. Conjugation experiments were performed using Escherichia coli and Staphylococcus aureus as receptors. Complete sequences of chromosomal DNA and plasmids were generated by whole genome sequencing (WGS) and bioinformatics analysis for the presence of drug resistance genes and mobile elements. Multidrug-resistant E. faecalis ESC1 contained a chromosome and three plasmids. The amino acid at position 80 of the parC gene on the chromosome was mutated from serine to isoleucine, and hence the amino acid mutation at this site led to the resistance of ESC1 strain to fluoroquinolones. Eleven antibiotic resistance genes were located on two plasmids. We identified a novel composite transposon carrying two aminoglycoside resistance genes aac(6')-aph(2″). This study reported the coexistence of a novel 5.4 kb composite transposon and a resistance plasmid with multiple homologous recombination in an isolate of E. faecalis ESC1. This data provides a basis for understanding the genomic signature and antimicrobial resistance mechanisms of this pathogen.
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Affiliation(s)
- Xue-Song Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Yu Qi
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Peng-hui Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Jun-ze Xue
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Xuan-yu Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Inam Muhammad
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
- Department of Zoology, Shaheed Benazir Bhutto University, Sheringal, Pakistan
| | - Ya-zhuo Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Dao-mi Zhu
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Ying Ma
- Liaoyuan Animal Disease Prevention and Control Center, Liaoyuan, China
| | - Ling-Cong Kong
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Hong-Xia Ma
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Changchun, China
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Monteiro Marques J, Coelho M, Santana AR, Pinto D, Semedo-Lemsaddek T. Dissemination of Enterococcal Genetic Lineages: A One Health Perspective. Antibiotics (Basel) 2023; 12:1140. [PMID: 37508236 PMCID: PMC10376465 DOI: 10.3390/antibiotics12071140] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/22/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Enterococcus spp. are commensals of the gastrointestinal tracts of humans and animals and colonize a variety of niches such as water, soil, and food. Over the last three decades, enterococci have evolved as opportunistic pathogens, being considered ESKAPE pathogens responsible for hospital-associated infections. Enterococci's ubiquitous nature, excellent adaptative capacity, and ability to acquire virulence and resistance genes make them excellent sentinel proxies for assessing the presence/spread of pathogenic and virulent clones and hazardous determinants across settings of the human-animal-environment triad, allowing for a more comprehensive analysis of the One Health continuum. This review provides an overview of enterococcal fitness and pathogenic traits; the most common clonal complexes identified in clinical, veterinary, food, and environmental sources; as well as the dissemination of pathogenic genomic traits (virulome, resistome, and mobilome) found in high-risk clones worldwide, across the One Health continuum.
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Affiliation(s)
- Joana Monteiro Marques
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Mariana Coelho
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Andressa Rodrigues Santana
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Daniel Pinto
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Teresa Semedo-Lemsaddek
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
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Ha HTA, Nguyen PTL, Hung TTM, Tuan LA, Thuy BT, Lien THM, Thai PD, Thanh NH, Bich VTN, Anh TH, Hanh NTH, Minh NT, Thanh DP, Mai SNT, The HC, Trung NV, Thu NH, Duong TN, Anh DD, Ngoc PT, Bañuls AL, Choisy M, van Doorn HR, Suzuki M, Hoang TH. Prevalence and Associated Factors of optrA-Positive- Enterococcus faecalis in Different Reservoirs around Farms in Vietnam. Antibiotics (Basel) 2023; 12:954. [PMID: 37370273 PMCID: PMC10294904 DOI: 10.3390/antibiotics12060954] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Linezolid is an antibiotic of last resort for the treatment of infections caused by Gram-positive bacteria, including vancomycin-resistant enterococci. Enterococcus faecalis, a member of enterococci, is a significant pathogen in nosocomial infections. E. faecalis resistance to linezolid is frequently related to the presence of optrA, which is often co-carried with fex, phenicol exporter genes, and erm genes encoding macrolide resistance. Therefore, the common use of antibiotics in veterinary might promote the occurrence of optrA in livestock settings. This is a cross-sectional study aiming to investigate the prevalence of optrA positive E. faecalis (OPEfs) in 6 reservoirs in farms in Ha Nam province, Vietnam, and its associated factors and to explore genetic relationships of OPEfs isolates. Among 639 collected samples, the prevalence of OPEfs was highest in flies, 46.8% (51/109), followed by chickens 37.3% (72/193), dogs 33.3% (17/51), humans 18.7% (26/139), wastewater 16.4% (11/67) and pigs 11.3%, (14/80). The total feeding area and total livestock unit of the farm were associated with the presence of OPEfs in chickens, flies, and wastewater. Among 186 OPEfs strains, 86% were resistant to linezolid. The presence of optrA was also related to the resistant phenotype against linezolid and levofloxacin of E. faecalis isolates. Close genotypic relationships identified by Pulsed Field Gel Electrophoresis between OPEfs isolates recovered from flies and other reservoirs including chickens, pigs, dogs, and wastewater suggested the role of flies in the transmission of antibiotic-resistant pathogens. These results provided warnings of linezolid resistance although it is not used in livestock.
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Affiliation(s)
- Hoang Thi An Ha
- Hanoi Medical University, Hanoi 100000, Vietnam; (H.T.A.H.); (T.H.A.)
- Department of Microbiology, Vinh Medical University, Vinh 431000, Vietnam
| | - Phuong Thi Lan Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Tran Thi Mai Hung
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Le Anh Tuan
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Bui Thanh Thuy
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Tran Hoang My Lien
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Pham Duy Thai
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Nguyen Ha Thanh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Vu Thi Ngoc Bich
- Oxford University Clinical Research Unit, Hanoi 100000, Vietnam; (V.T.N.B.); (H.R.v.D.)
| | - Tran Hai Anh
- Hanoi Medical University, Hanoi 100000, Vietnam; (H.T.A.H.); (T.H.A.)
| | - Ngo Thi Hong Hanh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Nguyen Thi Minh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Duy Pham Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam; (D.P.T.); (S.-N.T.M.); (H.C.T.)
| | - Si-Nguyen T. Mai
- Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam; (D.P.T.); (S.-N.T.M.); (H.C.T.)
| | - Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam; (D.P.T.); (S.-N.T.M.); (H.C.T.)
| | - Nguyen Vu Trung
- Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam;
| | | | - Tran Nhu Duong
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Pham Thi Ngoc
- National Institute of Veterinary Research, Hanoi 100000, Vietnam;
| | - Anne-Laure Bañuls
- MIVEGEC (IRD-CNRS-Université de Montpellier), LMI DRISA, Centre IRD, 34394 Montpellier, France;
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam; (D.P.T.); (S.-N.T.M.); (H.C.T.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 4BH, UK
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi 100000, Vietnam; (V.T.N.B.); (H.R.v.D.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 4BH, UK
| | - Masato Suzuki
- National Institute of Infectious Diseases, Tokyo 162-0052, Japan;
| | - Tran Huy Hoang
- Hanoi Medical University, Hanoi 100000, Vietnam; (H.T.A.H.); (T.H.A.)
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
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8
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Han N, Li J, Wan P, Pan Y, Xu T, Xiong W, Zeng Z. Co-Existence of Oxazolidinone Resistance Genes cfr(D) and optrA on Two Streptococcus parasuis Isolates from Swine. Antibiotics (Basel) 2023; 12:antibiotics12050825. [PMID: 37237728 DOI: 10.3390/antibiotics12050825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
This study was performed to investigate the presence and characteristics of the oxazolidinone resistance genes optrA and cfr(D) in Streptococcus parasuis. In total, 36 Streptococcus isolates (30 Streptococcus suis isolates, 6 Streptococcus parasuis isolates) were collected from pig farms in China in 2020-2021, using PCR to determine the presence of optrA and cfr. Then, 2 of the 36 Streptococcus isolates were further processed as follows. Whole-genome sequencing and de novo assembly were employed to analyze the genetic environment of the optrA and cfr(D) genes. Conjugation and inverse PCR were employed to verify the transferability of optrA and cfr(D). The optrA and cfr(D) genes were identified in two S. parasuis strains named SS17 and SS20, respectively. The optrA of the two isolates was located on chromosomes invariably associated with the araC gene and Tn554, which carry the resistance genes erm(A) and ant(9). The two plasmids that carry cfr(D), pSS17 (7550 bp) and pSS20-1 (7550 bp) have 100% nucleotide sequence identity. The cfr(D) was flanked by GMP synthase and IS1202. The findings of this study extend the current knowledge of the genetic background of optrA and cfr(D) and indicate that Tn554 and IS1202 may play an important role in the transmission of optrA and cfr(D), respectively.
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Affiliation(s)
- Ning Han
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jie Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Peng Wan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yu Pan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Tiantian Xu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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9
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Shen W, Huang Y, Cai J. An Optimized Screening Approach for the Oxazolidinone Resistance Gene optrA Yielded a Higher Fecal Carriage Rate among Healthy Individuals in Hangzhou, China. Microbiol Spectr 2022; 10:e0297422. [PMID: 36377960 PMCID: PMC9769644 DOI: 10.1128/spectrum.02974-22] [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] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/05/2022] [Indexed: 11/16/2022] Open
Abstract
The linezolid resistance mediated by optrA has exhibited an increasing trend among Gram-positive bacteria, which greatly limits the treatment options for severe bacterial infections. However, the prevalence of optrA was usually underestimated based on the existing screening methods. In this study, we used a traditional method and an improved method that included a high-salinity condition treatment after enrichment to screen for optrA-carrying bacteria from stool samples from 1,018 healthy donors in Hangzhou, China. The fecal carriage rate of optrA-carrying bacteria was 19.25% when screened by the improved method (196/1,018), which was much higher than that of the traditional method at 5.89% (60/1,018). Enterococci were the majority of the optrA-positive isolates, while five nonenterococcal isolates were also obtained, including two Streptococcus gallolyticus, one Vagococcus lutrae, one Lactococcus garvieae, and one Lactococcus formosensis isolate. Whole-genome sequencing analysis identified four novel OptrA variants, IDKKGPM, IDKKGP, KLDK, and EYDDI, in these isolates, whose optrA-flanking regions with a fexA gene downstream were bounded by different insertion sequences. In conclusion, our optimized method displayed high sensitivity in the detection of optrA-positive bacteria in fecal samples and revealed a high carriage rate in a healthy population. Although enterococci are dominant, multiple optrA-carrying Gram-positive bacteria were also found. IMPORTANCE This study represented an optimized screening approach for the optrA gene, which is an important mechanism of antimicrobial resistance to linezolid as a last resort for the treatment of infections caused by multiresistant Gram-positive bacteria. We revealed a high fecal carriage rate of the optrA gene among adults by this method and reported the first identification of optrA in Lactococcus formosensis as well as the identification of this gene in Vagococcus lutrae and of the poxtA gene in Ligilactobacillus salivarius of human origin, suggesting the wide spread of the optrA gene in the Gram-positive bacterial community.
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Affiliation(s)
- Weiyi Shen
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Yonglu Huang
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiachang Cai
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
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10
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Yang X, Zhang T, Lei CW, Wang Q, Huang Z, Chen X, Wang HN. Florfenicol and oxazolidone resistance status in livestock farms revealed by short- and long-read metagenomic sequencing. Front Microbiol 2022; 13:1018901. [PMID: 36338088 PMCID: PMC9632178 DOI: 10.3389/fmicb.2022.1018901] [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: 08/14/2022] [Accepted: 09/26/2022] [Indexed: 12/03/2022] Open
Abstract
Antibiotic resistance genes (ARGs) as a novel type of environmental pollutant pose a health risk to humans. Oxazolidinones are one of the most important antibiotics for the treatment of Gram-positive bacterial infections in humans. Although oxazolidinones are not utilized in the livestock industry, florfenicol is commonly used on farms to treat bacterial infections, which may contribute to the spread of the cfr, optrA, and poxtA genes on farms. Using metagenomics sequencing, we looked into the antibiotic resistome context of florfenicol and oxazolidinone in 10 large-scale commercial farms in China. We identified 490 different resistance genes and 1,515 bacterial genera in the fecal samples obtained from 10 farms. Florfenicol-resistant Kurthia, Escherichia, and Proteus were widely present in these samples. The situation of florfenicol and oxazolidone resistance in pig farms is even more severe. The total number of genes and the abundance of drug resistance genes were higher in pigs than in chickens, including optrA and poxtA. All the samples we collected had a high abundance of fexA and floR. Through nanopore metagenomic analysis of the genetic environment, we found that plasmids, integrative and conjugative element (ICE), and transposons (Tn7-like and Tn558) may play an important role in the spread of floR, cfr, and optrA. Our findings suggest that florfenicol and oxazolidinone resistance genes have diverse genetic environments and are at risk of co-transmission with, for example, tetracycline and aminoglycoside resistance genes. The spread of florfenicol- and oxazolidinone–resistant bacteria on animal farms should be continuously monitored.
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11
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Li P, Gao M, Feng C, Yan T, Sheng Z, Shi W, Liu S, Zhang L, Li A, Lu J, Lin X, Li K, Xu T, Bao Q, Sun C. Molecular characterization of florfenicol and oxazolidinone resistance in Enterococcus isolates from animals in China. Front Microbiol 2022; 13:811692. [PMID: 35958123 PMCID: PMC9360786 DOI: 10.3389/fmicb.2022.811692] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/07/2022] [Indexed: 11/24/2022] Open
Abstract
Florfenicol is widely used for the treatment of bacterial infections in domestic animals. The aim of this study was to analyze the molecular mechanisms of florfenicol and oxazolidinone resistance in Enterococcus isolates from anal feces of domestic animals. The minimum inhibitory concentration (MIC) levels were determined by the agar dilution method. Polymerase chain reaction (PCR) was performed to analyze the distribution of the resistance genes. Whole-genome sequencing and comparative plasmid analysis was conducted to analyze the resistance gene environment. A total of 351 non-duplicated enteric strains were obtained. Among these isolates, 22 Enterococcus isolates, including 19 Enterococcus. faecium and 3 Enterococcus. faecalis, were further studied. 31 florfenicol resistance genes (13 fexA, 3 fexB, 12 optrA, and 3 poxtA genes) were identified in 15 of the 19 E. faecium isolates, and no florfenicol or oxazolidinone resistance genes were identified in 3 E. faecalis isolates. Whole-genome sequencing of E. faecium P47, which had all four florfenicol and oxazolidinone resistance genes and high MIC levels for both florfenicol (256 mg/L) and linezolid (8 mg/L), revealed that it contained a chromosome and 3 plasmids (pP47-27, pP47-61, and pP47-180). The four florfenicol and oxazolidinone resistance genes were all related to the insertion sequences IS1216 and located on two smaller plasmids. The genes fexB and poxtA encoded in pP47-27, while fexA and optrA encoded in the conjugative plasmid pP47-61. Comparative analysis of homologous plasmids revealed that the sequences with high identities were plasmid sequences from various Enterococcus species except for the Tn6349 sequence from a Staphylococcus aureus chromosome (MH746818.1). The current study revealed that florfenicol and oxazolidinone resistance genes (fexA, fexB, poxtA, and optrA) were widely distributed in Enterococcus isolates from animal in China. The mobile genetic elements, including the insertion sequences and conjugative plasmid, played an important role in the horizontal transfer of florfenicol and oxazolidinone resistance.
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Affiliation(s)
- Pingping Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Nursing Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Department of Clinical Laboratory, Zhoukou Maternal and Child Health Hospital, Zhoukou, China
| | - Mengdi Gao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Tielun Yan
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhiqiong Sheng
- School of Nursing, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shuang Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lei Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Anqi Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
- Teng Xu,
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Qiyu Bao,
| | - Caixia Sun
- Nursing Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Caixia Sun,
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12
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Gião J, Leão C, Albuquerque T, Clemente L, Amaro A. Antimicrobial Susceptibility of Enterococcus Isolates from Cattle and Pigs in Portugal: Linezolid Resistance Genes optrA and poxtA. Antibiotics (Basel) 2022; 11:615. [PMID: 35625259 PMCID: PMC9137492 DOI: 10.3390/antibiotics11050615] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Enterococci are part of the commensal gut microbiota of mammals, with Enterococcus faecalis and Enterococcus faecium being the most clinically relevant species. This study assesses the prevalence and diversity of enterococcal species in cattle (n = 201) and pig (n = 249) cecal samples collected in 2017. Antimicrobial susceptibility profiles of E. faecium (n = 48) and E. faecalis (n = 84) were assessed by agar and microdilution methods. Resistance genes were screened through PCR and nine strains were analyzed by Whole Genome Sequencing. A wide range of enterococci species was found colonizing the intestines of pigs and cattle. Overall, the prevalence of resistance to critically important antibiotics was low (except for erythromycin), and no glycopeptide-resistant isolates were identified. Two daptomycin-resistant E. faecalis ST58 and ST93 were found. Linezolid-resistant strains of E. faecalis (n = 3) and E. faecium (n = 1) were detected. Moreover, oxazolidinone resistance determinants optrA (n = 8) and poxtA (n = 2) were found in E. faecalis (ST16, ST58, ST207, ST474, ST1178) and E. faecium (ST22, ST2138). Multiple variants of optrA were found in different genetic contexts, either in the chromosome or plasmids. We highlight the importance of animals as reservoirs of resistance genes to critically important antibiotics.
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Affiliation(s)
- Joana Gião
- Laboratory of Bacteriology and Mycology, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal; (J.G.); (C.L.); (T.A.); (L.C.)
- Department of Veterinary Medicine, University of Évora, 7002-554 Évora, Portugal
| | - Célia Leão
- Laboratory of Bacteriology and Mycology, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal; (J.G.); (C.L.); (T.A.); (L.C.)
- MED—Mediterranean Institute for Agriculture, Environment and Development, 7006-554 Évora, Portugal
| | - Teresa Albuquerque
- Laboratory of Bacteriology and Mycology, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal; (J.G.); (C.L.); (T.A.); (L.C.)
| | - Lurdes Clemente
- Laboratory of Bacteriology and Mycology, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal; (J.G.); (C.L.); (T.A.); (L.C.)
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Science, University of Lisbon, 1300-477 Lisboa, Portugal
| | - Ana Amaro
- Laboratory of Bacteriology and Mycology, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal; (J.G.); (C.L.); (T.A.); (L.C.)
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13
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Guffey AA, Loll PJ. Regulation of Resistance in Vancomycin-Resistant Enterococci: The VanRS Two-Component System. Microorganisms 2021; 9:2026. [PMID: 34683347 PMCID: PMC8541618 DOI: 10.3390/microorganisms9102026] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/20/2023] Open
Abstract
Vancomycin-resistant enterococci (VRE) are a serious threat to human health, with few treatment options being available. New therapeutics are urgently needed to relieve the health and economic burdens presented by VRE. A potential target for new therapeutics is the VanRS two-component system, which regulates the expression of vancomycin resistance in VRE. VanS is a sensor histidine kinase that detects vancomycin and in turn activates VanR; VanR is a response regulator that, when activated, directs expression of vancomycin-resistance genes. This review of VanRS examines how the expression of vancomycin resistance is regulated, and provides an update on one of the field's most pressing questions: How does VanS sense vancomycin?
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Affiliation(s)
| | - Patrick J. Loll
- Department of Biochemistry & Molecular Biology, College of Medicine, Drexel University, Philadelphia, PA 19102, USA;
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14
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Tang S, Yang R, Wu Q, Ding Y, Wang Z, Zhang J, Lei T, Wu S, Zhang F, Zhang W, Xue L, Zhang Y, Wei X, Pang R, Wang J. First report of the optrA-carrying multidrug resistance genomic island in Campylobacter jejuni isolated from pigeon meat. Int J Food Microbiol 2021; 354:109320. [PMID: 34229231 DOI: 10.1016/j.ijfoodmicro.2021.109320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/19/2022]
Abstract
Campylobacter spp., such as Campylobacter jejuni and Campylobacter coli, are important zoonotic Gram-negative pathogens that cause acute intestinal diseases in humans. The optrA gene, encoding an ATP-binding cassette F (ABC-F) protein that confers resistance to oxazolidinones and phenicols, has been found in C. coli in China. In this study, the optrA gene was first identified in C. jejuni collected from retail meat in China from 2013 to 2016. Nine strains, isolated from a pigeon meat sample, carry the optrA gene. The molecular characteristics of the optrA-positive strains were determined by whole genome sequencing. Pulsed-field gel electrophoresis, multilocus sequence typing, and single nucleotide polymorphism analyses demonstrated that the nine optrA-positive isolates were genetically homogeneous. Phylogenetic characteristics and sequence comparison revealed that optrA was located on a chromosome-borne multidrug resistance genomic island. The optrA gene along with the tet(O) gene formed two different translocatable units (TUs), thereby supporting the transmission of TU-associated resistance genes. The emergence and spread of such TUs and strains are of great concern in terms of food safety, and measures must be implemented to avoid their dissemination in other Gram-negative bacteria and food chains.
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Affiliation(s)
- Shengjun Tang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Runshi Yang
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Yu Ding
- Department of Food Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhi Wang
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Tao Lei
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Feng Zhang
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Weipei Zhang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Youxiong Zhang
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xianhu Wei
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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15
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Schwarz S, Zhang W, Du XD, Krüger H, Feßler AT, Ma S, Zhu Y, Wu C, Shen J, Wang Y. Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria. Clin Microbiol Rev 2021; 34:e0018820. [PMID: 34076490 PMCID: PMC8262807 DOI: 10.1128/cmr.00188-20] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Seven mobile oxazolidinone resistance genes, including cfr, cfr(B), cfr(C), cfr(D), cfr(E), optrA, and poxtA, have been identified to date. The cfr genes code for 23S rRNA methylases, which confer a multiresistance phenotype that includes resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A compounds. The optrA and poxtA genes code for ABC-F proteins that protect the bacterial ribosomes from the inhibitory effects of oxazolidinones. The optrA gene confers resistance to oxazolidinones and phenicols, while the poxtA gene confers elevated MICs or resistance to oxazolidinones, phenicols, and tetracycline. These oxazolidinone resistance genes are most frequently found on plasmids, but they are also located on transposons, integrative and conjugative elements (ICEs), genomic islands, and prophages. In these mobile genetic elements (MGEs), insertion sequences (IS) most often flanked the cfr, optrA, and poxtA genes and were able to generate translocatable units (TUs) that comprise the oxazolidinone resistance genes and occasionally also other genes. MGEs and TUs play an important role in the dissemination of oxazolidinone resistance genes across strain, species, and genus boundaries. Most frequently, these MGEs also harbor genes that mediate resistance not only to antimicrobial agents of other classes, but also to metals and biocides. Direct selection pressure by the use of antimicrobial agents to which the oxazolidinone resistance genes confer resistance, but also indirect selection pressure by the use of antimicrobial agents, metals, or biocides (the respective resistance genes against which are colocated on cfr-, optrA-, or poxtA-carrying MGEs) may play a role in the coselection and persistence of oxazolidinone resistance genes.
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Affiliation(s)
- Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Wanjiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
| | - Henrike Krüger
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Andrea T. Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Shizhen Ma
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yao Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Congming Wu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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Dutra MC, Moreno LZ, Dias RA, Moreno AM. Antimicrobial Use in Brazilian Swine Herds: Assessment of Use and Reduction Examples. Microorganisms 2021; 9:microorganisms9040881. [PMID: 33924277 PMCID: PMC8074920 DOI: 10.3390/microorganisms9040881] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022] Open
Abstract
Brazil, as a major pig producer, is currently experiencing the widespread use of antimicrobials as a serious issue to be addressed. For measures to be taken in this direction, the extent of the problem must be known. The goal of this study was to evaluate the use of antimicrobials in 25 Brazilian swine herds. Antimicrobial use from birth to slaughter was correlated with biosecurity and productivity. After the first assessment (2016; M0), 13 herds implemented good practices to reduce antimicrobial use. Four years after the implementation of these measures (2020; M1), data about antimicrobial usage from these herds were collected. The results of the first assessment (M0) demonstrated a troublesome scenario: the mean value of antimicrobials used was 358.4 mg/kg of pig produced; the median of the pig’s lifetime exposure to antimicrobials was 73.7%, and the median number of drugs used was seven. A positive correlation between the antimicrobials consumed and the pig’s antimicrobial exposure time was detected. Nevertheless, these data did not correlate with biosecurity score or productivity. A significant difference was detected in M1, where a median 30% reduction in antimicrobials consumed was detected. There was also a 44.3% reduction of the pig’s lifetime exposure to antimicrobials. The median number of drugs used was reduced from seven to five. Antimicrobial use did not always reflect the sanitary condition or the real therapeutic needs, easily leading to overuse.
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Almeida LM, Gaca A, Bispo PM, Lebreton F, Saavedra JT, Silva RA, Basílio-Júnior ID, Zorzi FM, Filsner PH, Moreno AM, Gilmore MS. Coexistence of the Oxazolidinone Resistance-Associated Genes cfr and optrA in Enterococcus faecalis From a Healthy Piglet in Brazil. Front Public Health 2020; 8:518. [PMID: 33102417 PMCID: PMC7546817 DOI: 10.3389/fpubh.2020.00518] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Oxazolidinones are one of the most important antimicrobials potentially active against glycopeptide- and β-lactam-resistant Gram-positive pathogens. Linezolid—the first oxazolidinone to be approved for clinical use in 2000 by the US Food and Drug Administration—and the newer molecule in the class, tedizolid, inhibit protein synthesis by suppressing the formation of the 70S ribosomal complex in bacteria. Over the past two decades, transferable oxazolidinone resistance genes, in particular cfr and optrA, have been identified in Firmicutes isolated from healthcare-related infections, livestock, and the environment. Our goals in this study were to investigate the genetic contexts and the transferability of the cfr and optrA genes and examine genomic features, such as antimicrobial resistance genes, plasmid incompatibility types, and CRISPR-Cas defenses of a linezolid-resistant Enterococcus faecalis isolated in feces from a healthy pig during an antimicrobial surveillance program for animal production in Brazil. The cfr gene was found to be integrated into a transposon-like structure of 7,759 nt flanked by IS1216E and capable of excising and circularizing, distinguishing it from known genetic contexts for cfr in Enterococcus spp., while optrA was inserted into an Inc18 broad host-range plasmid of >58 kb. Conjugal transfer of cfr and optrA was shown by filter mating. The coexistence of cfr and optrA in an E. faecalis isolated from a healthy nursery pig highlights the need for monitoring the use of antibiotics in the Brazilian swine production system for controlling spread and proliferation of antibiotic resistance.
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Affiliation(s)
- Lara M Almeida
- Institute of Pharmaceutical Sciences, Federal University of Alagoas, Maceió, Brazil.,Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Anthony Gaca
- Department of Ophthalmology and Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Paulo M Bispo
- Department of Ophthalmology and Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - François Lebreton
- Department of Ophthalmology and Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Jose T Saavedra
- Department of Ophthalmology and Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Rafael A Silva
- Institute of Pharmaceutical Sciences, Federal University of Alagoas, Maceió, Brazil
| | | | - Felipe M Zorzi
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Pedro H Filsner
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Andrea M Moreno
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Michael S Gilmore
- Department of Ophthalmology and Department of Microbiology, Harvard Medical School, Boston, MA, United States
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Drug Resistance Determinants in Clinical Isolates of Enterococcus faecalis in Bangladesh: Identification of Oxazolidinone Resistance Gene optrA in ST59 and ST902 Lineages. Microorganisms 2020; 8:microorganisms8081240. [PMID: 32824090 PMCID: PMC7463919 DOI: 10.3390/microorganisms8081240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/06/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022] Open
Abstract
Enterococcus faecalis is one of the major causes of urinary tract infection, showing acquired resistance to various classes of antimicrobials. The objective of this study was to determine the prevalence of drug resistance and its genetic determinants for E. faecalis clinical isolates in north-central Bangladesh. Among a total of 210 E. faecalis isolates, isolated from urine, the resistance rates to erythromycin, levofloxacin, and gentamicin (high level) were 85.2, 45.7, and 11.4%, respectively, while no isolates were resistant to ampicillin, vancomycin and teicoplanin. The most prevalent resistance gene was erm(B) (97%), and any of the four genes encoding aminoglycoside modifying enzyme (AME) were detected in 99 isolates (47%). The AME gene aac(6′)-Ie-aph(2”)-Ia was detected in 46 isolates (21.9%) and was diverse in terms of IS256-flanking patterns, which were associated with resistance level to gentamicin. Tetracycline resistance was ascribable to tet(M) (61%) and tet(L) (38%), and mutations in the quinolone resistance-determining region of both GyrA and ParC were identified in 44% of isolates. Five isolates (2.4%) exhibited non-susceptibility to linezolide (MIC, 4 μg/mL), and harbored the oxazolidinone resistance gene optrA, which was located in a novel genetic cluster containing the phenicol exporter gene fexA. The optrA-positive isolates belonged to ST59, ST902, and ST917 (CC59), while common lineages of other multiple drug-resistant isolates were ST6, ST28, CC16, and CC116. The present study first revealed the prevalence of drug resistance determinants of E. faecalis and their genetic profiles in Bangladesh.
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