1
|
Rebelo A, Almeida A, Peixe L, Antunes P, Novais C. Unraveling the Role of Metals and Organic Acids in Bacterial Antimicrobial Resistance in the Food Chain. Antibiotics (Basel) 2023; 12:1474. [PMID: 37760770 PMCID: PMC10525130 DOI: 10.3390/antibiotics12091474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
Antimicrobial resistance (AMR) has a significant impact on human, animal, and environmental health, being spread in diverse settings. Antibiotic misuse and overuse in the food chain are widely recognized as primary drivers of antibiotic-resistant bacteria. However, other antimicrobials, such as metals and organic acids, commonly present in agri-food environments (e.g., in feed, biocides, or as long-term pollutants), may also contribute to this global public health problem, although this remains a debatable topic owing to limited data. This review aims to provide insights into the current role of metals (i.e., copper, arsenic, and mercury) and organic acids in the emergence and spread of AMR in the food chain. Based on a thorough literature review, this study adopts a unique integrative approach, analyzing in detail the known antimicrobial mechanisms of metals and organic acids, as well as the molecular adaptive tolerance strategies developed by diverse bacteria to overcome their action. Additionally, the interplay between the tolerance to metals or organic acids and AMR is explored, with particular focus on co-selection events. Through a comprehensive analysis, this review highlights potential silent drivers of AMR within the food chain and the need for further research at molecular and epidemiological levels across different food contexts worldwide.
Collapse
Affiliation(s)
- Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- ESS, Polytechnic of Porto, 4200-072 Porto, Portugal
| | - Agostinho Almeida
- LAQV/REQUIMTE, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Faculty of Nutrition and Food Sciences (FCNAUP), University of Porto, 4150-180 Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| |
Collapse
|
2
|
Kusumoto M, Tamamura-Andoh Y, Hikoda-Kogiku Y, Magome A, Okuhama E, Sato K, Mizuno Y, Arai N, Watanabe-Yanai A, Iwata T, Ogura Y, Gotoh Y, Nakamura K, Hayashi T, Akiba M. Nationwide analysis of antimicrobial resistance in pathogenic Escherichia coli strains isolated from diseased swine over 29 years in Japan. Front Microbiol 2023; 14:1107566. [PMID: 37007495 PMCID: PMC10065406 DOI: 10.3389/fmicb.2023.1107566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Pathogenic Escherichia coli strains are important causes of several swine diseases that result in significant economic losses worldwide. In Japan, the use of antimicrobials in swine is much higher than that in other farm animals every year. Antimicrobial resistance in pathogenic E. coli strains also heavily impacts the swine industry due to the limited treatment options and an increase in the potential risk of the One Health crisis. In 2016, we investigated 684 Japanese isolates of swine pathogenic E. coli belonging to four major serogroups and reported the emergence and increase in the highly multidrug-resistant serogroups O116 and OSB9 and the appearance of colistin-resistant strains. In the present study, by expanding our previous analysis, we determined the serotypes and antimicrobial resistance of 1,708 E. coli strains isolated from diseased swine between 1991 and 2019 in Japan and found recent increases in the prevalences of multidrug-resistant strains and minor serogroup strains. Among the antimicrobials examined in this study that have been approved for animal use, a third-generation cephalosporin was found to be effective against the most isolates (resistance rate: 1.2%) but not against highly multidrug-resistant strains. We also analyzed the susceptibilities of the 1,708 isolates to apramycin and bicozamycin, both which are available for treating swine in Japan, and found that the rates of resistance to apramycin and bicozamycin were low (6.7% and 5.8%, respectively), and both antimicrobials are more effective (resistance rates: 2.7% and 5.4%, respectively) than third-generation cephalosporins (resistance rate: 16.2%) against highly multidrug-resistant strains.
Collapse
Affiliation(s)
- Masahiro Kusumoto
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
- Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
- *Correspondence: Masahiro Kusumoto,
| | - Yukino Tamamura-Andoh
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | | | - Asami Magome
- Kagoshima Central Livestock Hygiene Service Center, Kagoshima, Japan
| | - Erina Okuhama
- Miyazaki Livestock Hygiene Service Center, Miyazaki, Japan
| | - Keisuke Sato
- Niigata Chuo Livestock Hygiene Service Center, Niigata, Japan
| | - Yoshino Mizuno
- Kumamoto Chuo Livestock Hygiene Service Center, Kumamoto, Japan
| | - Nobuo Arai
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Ayako Watanabe-Yanai
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Taketoshi Iwata
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Yoshitoshi Ogura
- Department of Infectious Medicine, Kurume University School of Medicine, Fukuoka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masato Akiba
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| |
Collapse
|
3
|
Genetic and phenotypic analyses of mcr-harboring extended-spectrum β-lactamase-producing Escherichia coli isolates from companion dogs and cats in Japan. Vet Microbiol 2023; 280:109695. [PMID: 36848815 DOI: 10.1016/j.vetmic.2023.109695] [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: 10/30/2022] [Revised: 01/17/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023]
Abstract
The emergence of mcr plasmid-mediated colistin-resistant extended-spectrum β-lactamase (ESBL)-producing Enterobacterales among companion dogs and cats poses a risk of the animals acting as reservoirs for cross-species transmission. However, current knowledge of mcr-harboring ESBL-producing Enterobacterales in companion dogs and cats is still limited; thus, the genetic and phenotypic characteristics of the bacterial isolates and plasmids, in companion dogs and cats, remain to be elucidated. Here, we identified mcr gene-harboring ESBL-producing Escherichia coli isolates during whole-genome sequencing of ESBL-producing E. coli isolates from a dog and a cat in Osaka, Japan. Colistin-resistant MY732 isolate from a dog carried two plasmids: mcr-1.1-harboring IncI2 plasmid and blaCTX-M-14-harboring IncFIB plasmid. Conjugation assays revealed that both plasmids can be co-transferred even though the IncFIB plasmid lacked a conjugal transfer gene cassette. The other isolate MY504 from a cat harbored two bla genes and mcr-9 on the identical IncHI2 plasmid. This isolate was not resistant to colistin, which is likely to be due to deletion of the regulatory two-component QseBC system associated with the mcr-9 expression. To the best of our knowledge, this is the first report of a colistin-resistant ESBL-producing E. coli isolate harboring mcr-1 from a companion dog in Japan. Given that the mcr gene-harboring IncI2 and IncHI2 plasmids in this study shared high homology with plasmids from human or animal-derived Enterobacterales, companion dogs and cats may act as important reservoirs for cross-species transmission of the mcr gene in the community, in Japan.
Collapse
|
4
|
Kakita T, Shigemura H, Fukuda A, Katamune C, Nidaira M, Kudeken T, Kyan H. Antimicrobial resistance and molecular epidemiological analysis of Escherichia fergusonii harboring the mcr gene in pigs and broiler chickens in Okinawa, Japan. J Vet Med Sci 2023; 85:149-156. [PMID: 36504025 PMCID: PMC10017296 DOI: 10.1292/jvms.22-0288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The dissemination of mcr-harboring Enterobacteriaceae, e.g., Escherichia fergusonii, with resistance to colistin via animal products is a public health concern. In our previous study, E. fergusonii harboring the mcr gene were isolated from 11 pigs and 43 chickens. To understand the spread of mcr-harboring E. fergusonii in Okinawa, Japan, and to gain further insights into how they can be controlled, an antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), a conjugation test for the transferability of mcr-harboring plasmids, and PCR-based replicon typing (PBRT) were performed using the 54 strains. According to the disk-diffusion and broth microdilution methods, 9 of the 11 strains from pigs and 9 of the 43 strains from chickens had multidrug resistance (MDR). The broth microdilution method showed that all strains were resistant to colistin, and the minimum inhibitory concentration of colistin was 4-16 μg/mL. PFGE suggested identical PFGE types were being transmitted within one pig farm, within one chicken farm, and among several chicken farms. These findings showed that some mcr-harboring E. fergusonii in Okinawa exhibited MDR, and these had spread within farms and between farms. In the mcr gene conjugation test and PBRT, a type IncI2 plasmid replicon was detected in all mcr-1-harboring transconjugants. Therefore, evidence suggests that the IncI2 plasmid is probably involved in the transmission of the mcr-1 gene. It is important to monitor the antimicrobial resistance profile and dissemination of the IncI2 plasmid in mcr-harboring E. fergusonii.
Collapse
Affiliation(s)
- Tetsuya Kakita
- Department of Biological Sciences, Okinawa Prefectural Institute of Health and Environment, Okinawa, Japan
| | - Hiroaki Shigemura
- Division of Pathology and Microbiology, Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Akira Fukuda
- Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan
| | - Chiharu Katamune
- Division of Pathology and Microbiology, Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Minoru Nidaira
- Department of Biological Sciences, Okinawa Prefectural Institute of Health and Environment, Okinawa, Japan
| | - Tsuyoshi Kudeken
- Department of Biological Sciences, Okinawa Prefectural Institute of Health and Environment, Okinawa, Japan
| | - Hisako Kyan
- Department of Biological Sciences, Okinawa Prefectural Institute of Health and Environment, Okinawa, Japan
| |
Collapse
|
5
|
Ben Haj Yahia A, Tayh G, Landolsi S, Maamar E, Galai N, Landoulsi Z, Messadi L. First Report of OXA-48 and IMP Genes Among Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates from Diarrheic Calves in Tunisia. Microb Drug Resist 2023; 29:150-162. [PMID: 36695709 DOI: 10.1089/mdr.2022.0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Antimicrobial resistance is one of the most serious threats to human and animal health. Evidence suggests that the overuse of antimicrobial agents in animal production has led to the emergence and dissemination of multidrug-resistant isolates. The objective of this study was to assess the rate of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in calf feces and to characterize their resistance genes for antibiotics like beta-lactams and colistin, but also to determine their virulence genes. Fecal samples were collected from 100 diarrheic calves in the region of Bizerte, Tunisia. After isolation, E. coli isolates were screened for antimicrobial resistance against 21 antibiotics by the disc diffusion method. Characterization of β-lactamase genes and determination of associated resistance genes were performed by polymerase chain reaction. Among 71 E. coli isolates, 26 (36.6%) strains were ESBL-producing. Most of these isolates were multidrug-resistant (92.3%) and the most prevalent beta-lactamase genes detected were blaCTX-M (n = 26), blaSHV (n = 11), and blaTEM (n = 8), whereas only 1 isolate carried the blaCMY gene. In addition, resistance to carbapenems was detected in two isolates; one of them harbored both blaOXA-48 and blaIMP genes and the other isolate carried only the blaIMP gene. Several resistance genes were identified for the first time in Tunisia from cases of diarrheic calves. Furthermore, to the best of our knowledge, this is the first report of detection and identification of carbapenem resistance genes and virulence genes from calves in North Africa. A high occurrence of antimicrobial resistance of E. coli recovered from fecal samples of calves with diarrhea was observed, highlighting the need for prudent use of antimicrobial agents in veterinary medicine to decrease the incidence of multidrug-resistant bacteria for both animals and humans.
Collapse
Affiliation(s)
- Asma Ben Haj Yahia
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisie.,Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, University of Tunis El Manar, Tunis, Tunisie
| | - Ghassan Tayh
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisie.,Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, University of Tunis El Manar, Tunis, Tunisie
| | - Sarrah Landolsi
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisie
| | - Elaa Maamar
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisie
| | - Nejia Galai
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisie
| | - Zbaida Landoulsi
- Office des Terres Domaniales, Agrocombinat Ghezala, Mateur, Tunisie
| | - Lilia Messadi
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisie
| |
Collapse
|
6
|
Jang H, Eshwar A, Lehner A, Gangiredla J, Patel IR, Beaubrun JJG, Chase HR, Negrete F, Finkelstein S, Weinstein LM, Ko K, Addy N, Ewing L, Woo J, Lee Y, Seo K, Jaradat Z, Srikumar S, Fanning S, Stephan R, Tall BD, Gopinath GR. Characterization of Cronobacter sakazakii Strains Originating from Plant-Origin Foods Using Comparative Genomic Analyses and Zebrafish Infectivity Studies. Microorganisms 2022; 10:microorganisms10071396. [PMID: 35889115 PMCID: PMC9319161 DOI: 10.3390/microorganisms10071396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA hybridization analyses using a pan-genomic microarray showed that these strains clustered according to sequence types (STs) identified by multi-locus sequence typing (MLST). PHASTER analysis identified 185 intact prophage gene clusters encompassing 22 different prophages, including three intact Cronobacter prophages: ENT47670, ENT39118, and phiES15. AMRFinderPlus analysis identified the CSA family class C β-lactamase gene in all strains and a plasmid-borne mcr-9.1 gene was identified in three strains. ZI studies showed that some plant-origin C. sakazakii display virulence comparable to clinical strains. Finding virulent plant-origin C. sakazakii possessing significant genomic features of clinically relevant STs suggests that these foods can serve as potential transmission vehicles and supports widening the scope of continued surveillance for this important foodborne pathogen.
Collapse
Affiliation(s)
- Hyein Jang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Athmanya Eshwar
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Jayanthi Gangiredla
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Isha R. Patel
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Junia Jean-Gilles Beaubrun
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Hannah R. Chase
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Flavia Negrete
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Samantha Finkelstein
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Leah M. Weinstein
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Katie Ko
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Nicole Addy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Laura Ewing
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Jungha Woo
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Youyoung Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Kunho Seo
- Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea;
| | - Ziad Jaradat
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Shabarinath Srikumar
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin & WHO Collaborating Centre for Cronobacter, Belfield, D04 N2E5 Dublin, Ireland; (S.S.); (S.F.)
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin & WHO Collaborating Centre for Cronobacter, Belfield, D04 N2E5 Dublin, Ireland; (S.S.); (S.F.)
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Ben D. Tall
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
- Correspondence: (B.D.T.); (G.R.G.)
| | - Gopal R. Gopinath
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
- Correspondence: (B.D.T.); (G.R.G.)
| |
Collapse
|
7
|
Khuntayaporn P, Thirapanmethee K, Chomnawang MT. An Update of Mobile Colistin Resistance in Non-Fermentative Gram-Negative Bacilli. Front Cell Infect Microbiol 2022; 12:882236. [PMID: 35782127 PMCID: PMC9248837 DOI: 10.3389/fcimb.2022.882236] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/16/2022] [Indexed: 12/14/2022] Open
Abstract
Colistin, the last resort for multidrug and extensively drug-resistant bacterial infection treatment, was reintroduced after being avoided in clinical settings from the 1970s to the 1990s because of its high toxicity. Colistin is considered a crucial treatment option for Acinetobacter baumannii and Pseudomonas aeruginosa, which are listed as critical priority pathogens for new antibiotics by the World Health Organization. The resistance mechanisms of colistin are considered to be chromosomally encoded, and no horizontal transfer has been reported. Nevertheless, in November 2015, a transmissible resistance mechanism of colistin, called mobile colistin resistance (MCR), was discovered. Up to ten families with MCR and more than 100 variants of Gram-negative bacteria have been reported worldwide. Even though few have been reported from Acinetobacter spp. and Pseudomonas spp., it is important to closely monitor the epidemiology of mcr genes in these pathogens. Therefore, this review focuses on the most recent update on colistin resistance and the epidemiology of mcr genes among non-fermentative Gram-negative bacilli, especially Acinetobacter spp. and P. aeruginosa.
Collapse
Affiliation(s)
- Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- *Correspondence: Piyatip Khuntayaporn,
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Mullika Traidej Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| |
Collapse
|
8
|
Sasaki Y, Kakizawa H, Baba Y, Ito T, Haremaki Y, Yonemichi M, Ikeda T, Kuroda M, Ohya K, Hara-Kudo Y, Asai T, Asakura H. Antimicrobial Resistance in Salmonella Isolated from Food Workers and Chicken Products in Japan. Antibiotics (Basel) 2021; 10:antibiotics10121541. [PMID: 34943753 PMCID: PMC8698854 DOI: 10.3390/antibiotics10121541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
Salmonella is an enteric bacterial pathogen that causes foodborne illness in humans. Third-generation cephalosporin (TGC) resistance in Salmonella remains a global concern. Food workers may represent a reservoir of Salmonella, thus potentially contaminating food products. Therefore, we aimed to investigate the prevalence of Salmonella in food workers and characterize the isolates by serotyping and antimicrobial susceptibility testing. Salmonella was isolated from 583 (0.079%) of 740,635 stool samples collected from food workers between January and December 2018, and then serotyped into 76 Salmonella enterica serovars and 22 untypeable Salmonella strains. High rates of antimicrobial resistance were observed for streptomycin (51.1%), tetracycline (33.1%), and kanamycin (18.4%). Although isolates were susceptible to ciprofloxacin, 12 (2.1%) strains (one S. Infantis, one S. Manhattan, two S. Bareilly, two S. Blockley, two S. Heidelberg, two S. Minnesota, one S. Goldcoast, and one untypeable Salmonella strain) were resistant to the TGC cefotaxime, all of which harbored β-lactamase genes (blaCMY-2, blaCTX-M-15, blaCTX-M-55, and blaTEM-52B). Moreover, 1.3% (4/309) of Salmonella strains (three S. Infantis and one S. Manhattan strains) isolated from chicken products were resistant to cefotaxime and harbored blaCMY-2 or blaTEM-52B. Thus, food workers may acquire TGC-resistant Salmonella after the ingestion of contaminated chicken products and further contaminate food products.
Collapse
Affiliation(s)
- Yoshimasa Sasaki
- Division of Biomedical Food Research, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki 210-9501, Kanagawa, Japan;
- Department of Applied Veterinary Science, The United Graduate School of Veterinary Science, Gifu University, 1-1, Yanagido, Gifu 501-1193, Gifu, Japan;
- Correspondence: ; Tel.: +81-44-270-6566; Fax: +81-44-270-6569
| | - Hiromi Kakizawa
- Incorporated Foundation Tokyo Kenbikyo-in, 1-100-38 Takamatsu-cho, Tachikawa 190-0011, Tokyo, Japan; (H.K.); (Y.B.); (T.I.)
| | - Youichi Baba
- Incorporated Foundation Tokyo Kenbikyo-in, 1-100-38 Takamatsu-cho, Tachikawa 190-0011, Tokyo, Japan; (H.K.); (Y.B.); (T.I.)
| | - Takeshi Ito
- Incorporated Foundation Tokyo Kenbikyo-in, 1-100-38 Takamatsu-cho, Tachikawa 190-0011, Tokyo, Japan; (H.K.); (Y.B.); (T.I.)
| | - Yukari Haremaki
- BML Food Science Solutions, Inc., 1549-7, Matoba, Kawagoe 350-1101, Saitama, Japan; (Y.H.); (M.Y.)
| | - Masaru Yonemichi
- BML Food Science Solutions, Inc., 1549-7, Matoba, Kawagoe 350-1101, Saitama, Japan; (Y.H.); (M.Y.)
| | - Tetsuya Ikeda
- Department of Infectious Diseases, Hokkaido Institute of Public Health, Kita19 Nishi 12, Kita-ku, Sapporo 060-0819, Hokkaido, Japan;
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan;
| | - Kenji Ohya
- Division of Microbiology, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki 210-9501, Kanagawa, Japan; (K.O.); (Y.H.-K.)
| | - Yukiko Hara-Kudo
- Division of Microbiology, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki 210-9501, Kanagawa, Japan; (K.O.); (Y.H.-K.)
| | - Tetsuo Asai
- Department of Applied Veterinary Science, The United Graduate School of Veterinary Science, Gifu University, 1-1, Yanagido, Gifu 501-1193, Gifu, Japan;
| | - Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki 210-9501, Kanagawa, Japan;
- Department of Applied Veterinary Science, The United Graduate School of Veterinary Science, Gifu University, 1-1, Yanagido, Gifu 501-1193, Gifu, Japan;
| |
Collapse
|
9
|
Yu Y, Hu B, Fan H, Zhang H, Lian S, Li H, Li S, Yan X, Wang S, Bai X. Molecular Epidemiology of Extraintestinal Pathogenic Escherichia coli Causing Hemorrhagic Pneumonia in Mink in Northern China. Front Cell Infect Microbiol 2021; 11:781068. [PMID: 34778114 PMCID: PMC8581539 DOI: 10.3389/fcimb.2021.781068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
The molecular epidemiology and biological characteristics of Escherichia coli associated with hemorrhagic pneumonia (HP) mink from five Chinese Provinces were determined. From 2017 to 2019, 85 E. coli strains were identified from 115 lung samples of mink suffering from HP. These samples were subjected to serotyping, antimicrobial susceptibility, detection of virulence genes, phylogenetic grouping, whole-genome sequencing, drug resistant gene, multilocus sequence typing (MLST) and biofilm-forming assays. E. coli strains were divided into 18 serotypes. Thirty-nine E. coli strains belonged to the O11 serotype. Eighty-five E. coli strains were classified into seven phylogenetic groups: E (45.9%, 39/85), A (27.1%, 23/85), B1 (14.1%, 12/85), B2 (3.7%, 3/85), D (3.7%, 3/85), F (2.4%, 2/85) and clade I (1.2%, 1/85). MLST showed that the main sequence types (STs) were ST457 (27/66), All E. coli strains had ≥4 virulence genes. The prevalence of virulence was 98.8% for yijp and fimC, 96.5% for iucD, 95.3% for ompA, 91.8% for cnf-Ⅰ, 89.4% for mat, 82.3% for hlyF, and 81.2% for ibeB. The prevalence of virulence genes iss, cva/cvi, aatA, ibeA, vat, hlyF, and STa was 3.5-57.6%. All E. coli strains were sensitive to sulfamethoxazole, but high resistance was shown to tetracycline (76.5%), chloramphenicol (71.8%), ciprofloxacin (63.5%) and florfenicol (52.9%), resistance to other antibiotics was 35.3-16.5%. The types and ratios of drug-resistance genes were tet(A), strA, strB, sul2, oqxA, blaTEM-1B, floR, and catA1 had the highest frequency from 34%-65%, which were consistent with our drug resistance phenotype tetracycline, florfenicol, quinolones, chloramphenicol, the bla-NDM-I and mcr-I were presented in ST457 strains. Out of 85 E. coli strains, six (7.1%) possessed a strong ability, 12 (14.1%) possessed a moderate ability, and 64 (75.3%) showed a weak ability to form biofilm. Our data will aid understanding of the epidemiological background and provide a clinical basis for HP treatment in mink caused by E. coli.
Collapse
Affiliation(s)
- Ying Yu
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bo Hu
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Huanhuan Fan
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Hailing Zhang
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shizhen Lian
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Hongye Li
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shuangshuang Li
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xijun Yan
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shaohui Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xue Bai
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| |
Collapse
|
10
|
Girardello R, Piroupo CM, Martins J, Maffucci MH, Cury AP, Franco MRG, Malta FDM, Rocha NC, Pinho JRR, Rossi F, Duarte AJDS, Setubal JC. Genomic Characterization of mcr-1.1-Producing Escherichia coli Recovered From Human Infections in São Paulo, Brazil. Front Microbiol 2021; 12:663414. [PMID: 34177843 PMCID: PMC8221240 DOI: 10.3389/fmicb.2021.663414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/12/2021] [Indexed: 11/25/2022] Open
Abstract
Polymyxins are one of most important antibiotics available for multidrug-resistant Gram-negative infections. Diverse chromosomal resistance mechanisms have been described, but the polymyxin resistance phenotype is not yet completely understood. The objective of this study was to characterize colistin resistant mcr-1-producing strains isolated from human infections over one year in a hospital setting (Hospital das Clínicas, São Paulo, Brazil). We isolated 490 colistin-resistant Gram-negative rods, of which eight were mcr-1.1-positive Escherichia coli, the only species with this result, indicating a low incidence of the mcr-1 production mechanism among colistin-resistant isolates. All mcr-1.1 positive isolates showed similarly low MICs for colistin and were susceptible to most antibiotics tested. The isolates showed diversity of MLST classification. The eight mcr-1.1-positive E. coli genomes were sequenced. In seven of eight isolates the mcr-1.1 gene is located in a contig that is presumed to be a part of an IncX4 plasmid; in one isolate, it is located in a contig that is presumed to be part of an IncHI2A plasmid. Three different genomic contexts for mcr-1.1 were observed, including a genomic cassette mcr-1.1-pap2 disrupting a DUF2806 domain-containing gene in six isolates. In addition, an IS1-family transposase was found inserted next to the mcr-1.1 cassette in one isolate. An mcr-1.1-pap2 genomic cassette not disrupting any gene was identified in another isolate. Our results suggest that plasmid dissemination of hospital-resident strains took place during the study period and highlight the need for continued genomic surveillance.
Collapse
Affiliation(s)
- Raquel Girardello
- Laboratório de Microbiologia Molecular e Clínica, Programa de Pós-Graduação em Ciências da Saúde, Universidade São Francisco, Braganca Paulista, Brazil
| | - Carlos Morais Piroupo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Joaquim Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Marcia Helena Maffucci
- Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Ana Paula Cury
- Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Renata Gomes Franco
- Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Natália Conceição Rocha
- Laboratório de Microbiologia Molecular e Clínica, Programa de Pós-Graduação em Ciências da Saúde, Universidade São Francisco, Braganca Paulista, Brazil.,Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - João Renato Rebello Pinho
- Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Técnicas Especiais, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Flavia Rossi
- Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Alberto José da Silva Duarte
- Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
11
|
Nagy Á, Székelyhidi R, Hanczné Lakatos E, Kapcsándi V. Review on the occurrence of the mcr-1 gene causing colistin resistance in cow's milk and dairy products. Heliyon 2021; 7:e06800. [PMID: 33898852 PMCID: PMC8060599 DOI: 10.1016/j.heliyon.2021.e06800] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/25/2021] [Accepted: 04/10/2021] [Indexed: 01/17/2023] Open
Abstract
Both livestock farmers and the clinic use significant amount of antibiotics worldwide, in many cases the same kind. Antibiotic resistance is not a new phenomenon, however, it is a matter of concern that resistance genes (mcr - Mobilized Colistin Resistance - genes) that render last-resort drugs (Colistin) ineffective, have already evolved. Nowadays, there is a significant consumption of milk and dairy products, which, if not treated properly, can contain bacteria (mainly Gram-negative bacteria). We collected articles and reviews in which Gram-negative bacteria carrying the mcr-1 gene have been detected in milk, dairy products, or cattle. Reports have shown that although the incidence is still low, unfortunately the gene has been detected in some dairy products on almost every continent. In the interest of our health, the use of colistin in livestock farming must be banned as soon as possible, and new treatments should be applied so that we can continue to have a chance in fighting multidrug-resistant bacteria in human medicine.
Collapse
|
12
|
Moon DC, Kim SJ, Mechesso AF, Kang HY, Song HJ, Choi JH, Yoon SS, Lim SK. Mobile Colistin Resistance Gene mcr- 1 Detected on an IncI2 Plasmid in Salmonella Typhimurium Sequence Type 19 from a Healthy Pig in South Korea. Microorganisms 2021; 9:398. [PMID: 33671955 PMCID: PMC7919004 DOI: 10.3390/microorganisms9020398] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 01/21/2023] Open
Abstract
Colistin is considered the last resort for the treatment of multi-drug resistant Gram-negative bacterial infections. We studied colistin resistance and the mcr-1 gene carriage in Salmonella isolates recovered from food animals in South Korea between 2010 and 2018. Colistin resistance was found in 277 isolates, predominantly in Salmonella Enteritidis (57.1%) and Salmonella Gallinarum (41.9%). However, the mcr-1 gene was identified in only one colistin-resistant Salmonella Typhimurium (MIC = 16 µg/mL) isolated from a healthy pig. The mcr-1 carrying isolate presented additional resistance to multiple antimicrobials. The strain belonged to sequence type (ST)19 and carried various virulence factor genes that are associated with adhesion and invasion of Salmonella into intestinal epithelial cells, as well as its survival in macrophages. The mcr-1 gene was identified on an IncI2 plasmid and it was also transferred to the E. coli J53 recipient strain. The mcr-1-carrying plasmid (pK18JST013) in this study was closely related to that previously reported in S. Indiana (pCFSA664-3) from chicken in China. This is the first report of mcr-1 carrying S. Typhimurium in South Korea. The finding indicates the importance of regular screening for the presence of the mcr-1 gene in S. Typhimurium in food animals to prevent the spread to humans.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si 39660, Korea; (D.C.M.); (S.-J.K.); (A.F.M.); (H.Y.K.); (H.-J.S.); (J.-H.C.); (S.-S.Y.)
| |
Collapse
|
13
|
Shafiq M, Huang J, Shah JM, Wang X, Rahman SU, Ali I, Chen L, Wang L. Characterization and virulence factors distribution of bla CTX-M and mcr-1carrying Escherichia coli isolates from bovine mastitis. J Appl Microbiol 2021; 131:634-646. [PMID: 33411963 DOI: 10.1111/jam.14994] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 11/26/2022]
Abstract
AIM To investigate the occurrence of ESBL and colistin-resistant E. coli and its genotypic characterization and identification of virulence determinants in cases of bovine mastitis in three provinces of China. MATERIALS AND METHODS Five hundred and thirty-five milk samples presenting mastitis symptoms were screened for the presence of ESBL, colistin-resistant and different virulence genes. Susceptibility testing was identified by the micro-dilution method. Escherichia coli isolates were used to detect ESBL genes (blaCTX-M , blaSHV and blaTEM ) and colistin-resistant genes mcr-(1-9). Multiplex PCR approach was used for the detection of major blaCTX-M groups, different phylogroups and virulence genes. The clonal relationship was then evaluated with MLST, MLSA and PFGE. RESULTS Multi-drug resistance (MDR) was found in more than 85% of ESBL and colistin-resistant E. coli isolates. Genotypic characterization showed a dominance of the blaCTX-M-1 group, and the most prevalent alleles observed were blaCTX-M-28 (38·37%), blaCTX-M-14 (17·44%), blaCTX-M-66 (13·95%) and blaCTX-M-55 (10·46%). The targeted virulence genes were detected in 97·89% of isolates. Sequence types ST58 and ST410 were the most predominant (2/20 = 20%). The majority of the E. coli isolates carrying ESBL and mcr-1 were clonally unrelated. CONCLUSION High level of association was observed between ESBL-producing and COL-resistance in E. coli of bovine mastitis. SIGNIFICANCE AND IMPACT OF THE STUDY To the best of our knowledge, this is the first report which shows the genetic diversity of ESBL and mcr-1, and various virulent features of E. coli strains isolated from bovine clinical mastitis in three different provinces of China. The major carriers of the blaCTX-M-1 and blaCTX-M-9 were blaCTX-M-28 and blaCTX-M-14 alleles respectively. The association of ESBL-producing E. coli with mcr-1 is of particular concern.
Collapse
Affiliation(s)
- M Shafiq
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - J Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - J M Shah
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - X Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - S U Rahman
- College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Mardan, KP, Pakistan
| | - I Ali
- College of Animal Sciences, Nanjing Agricultural University, Nanjing, China
| | - L Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - L Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
14
|
Escherichia coli Sequence Type 457 Is an Emerging Extended-Spectrum-β-Lactam-Resistant Lineage with Reservoirs in Wildlife and Food-Producing Animals. Antimicrob Agents Chemother 2020; 65:AAC.01118-20. [PMID: 33020161 DOI: 10.1128/aac.01118-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/18/2020] [Indexed: 01/16/2023] Open
Abstract
Silver gulls carry phylogenetically diverse Escherichia coli, including globally dominant extraintestinal pathogenic E. coli (ExPEC) sequence types and pandemic ExPEC-ST131 clades; however, our large-scale study (504 samples) on silver gulls nesting off the coast of New South Wales identified E. coli ST457 as the most prevalent. A phylogenetic analysis of whole-genome sequences (WGS) of 138 ST457 samples comprising 42 from gulls, 2 from humans (Australia), and 14 from poultry farmed in Paraguay were compared with 80 WGS deposited in public databases from diverse sources and countries. E. coli ST457 strains are phylogenetic group F, carry fimH145, and partition into five main clades in accordance to predominant flagella H-antigen carriage. Although we identified considerable phylogenetic diversity among the 138 ST457 strains, closely related subclades (<100 SNPs) suggested zoonotic or zooanthroponosis transmission between humans, wild birds, and food-producing animals. Australian human clinical and gull strains in two of the clades were closely related (≤80 SNPs). Regarding plasmid content, country, or country/source, specific connections were observed, including I1/ST23, I1/ST314, and I1/ST315 disseminating bla CMY-2 in Australia, I1/ST113 carrying bla CTX-M-8 and mcr-5 in Paraguayan poultry, and F2:A-:B1 plasmids of Dutch origin being detected across multiple ST457 clades. We identified a high prevalence of nearly identical I1/ST23 plasmids carrying bla CMY-2 among Australian gull and clinical human strains. In summary, ST457 is a broad host range, geographically diverse E. coli lineage that can cause human extraintestinal disease, including urinary tract infection, and displays a remarkable ability to capture mobile elements that carry and transmit genes encoding resistance to critically important antibiotics.
Collapse
|
15
|
Shigemura H, Sakatsume E, Sekizuka T, Yokoyama H, Hamada K, Etoh Y, Carle Y, Mizumoto S, Hirai S, Matsui M, Kimura H, Suzuki M, Onozuka D, Kuroda M, Inoshima Y, Murakami K. Food Workers as a Reservoir of Extended-Spectrum-Cephalosporin-Resistant Salmonella Strains in Japan. Appl Environ Microbiol 2020; 86:e00072-20. [PMID: 32276982 PMCID: PMC7301857 DOI: 10.1128/aem.00072-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/07/2020] [Indexed: 11/20/2022] Open
Abstract
Dissemination of extended-spectrum-cephalosporin (ESC)-resistant Salmonella, especially extended-spectrum-β-lactamase (ESBL)-producing Salmonella, is a concern worldwide. Here, we assessed Salmonella carriage by food workers in Japan to clarify the prevalence of ESC-resistant Salmonella harboring blaCTX-M We then characterized the genetic features, such as transposable elements, of blaCTX-M-harboring plasmids using whole-genome sequencing. A total of 145,220 stool samples were collected from food workers, including cooks and servers from several restaurants, as well as food factory workers, from January to October 2017. Isolated salmonellae were subjected to antimicrobial susceptibility testing (disk diffusion method), and whole-genome sequencing was performed for Salmonella strains harboring blaCTX-M Overall, 164 Salmonella isolates (0.113%) were recovered from 164 samples, from which we estimated that at least 0.113% (95% confidence interval [CI]: 0.096 to 0.132%) of food workers may carry Salmonella Based on this estimation, 3,473 (95% CI = 2,962 to 4,047) individuals among the 3,075,330 Japanese food workers are likely to carry Salmonella Of the 158 culturable isolates, seven showed resistance to ESCs: three isolates harbored blaCMY-2 and produced AmpC β-lactamase, while four ESBL-producing isolates harbored blaCTX-M-14 (n = 1, Salmonella enterica serovar Senftenberg) or blaCTX-M-15 (n = 3, S. enterica serovar Haardt). blaCTX-M-15 was chromosomally located in the S Haardt isolates, which also contained ISEcp1, while the S Senftenberg isolate contained an IncFIA(HI1)/IncHI1A/IncHI1B(R27) hybrid plasmid carrying blaCTX-M-14 along with ISEcp1 This study indicates that food workers may be a reservoir of ESBL-producing Salmonella and associated genes. Thus, these workers may contribute to the spread of blaCTX-M via plasmids or mobile genetic elements such as ISEcp1IMPORTANCE Antimicrobial-resistant Salmonella bacteria arise in farm environments through imprudent use of antimicrobials. Subsequently, these antimicrobial-resistant strains, such as extended-spectrum-β-lactamase (ESBL)-producing Salmonella, may be transmitted to humans via food animal-derived products. Here, we examined Salmonella carriage among food handlers in Japan. Overall, 164 of 145,220 fecal samples (0.113%) were positive for Salmonella Among the 158 tested isolates, four were identified as ESBL-producing isolates carrying ESBL determinants blaCTX-M-15 or blaCTX-M-14 In all cases, the genes coexisted with ISEcp1, regardless of whether they were located on the chromosome or on a plasmid. Our findings suggest that food workers may be a reservoir of ESBL-producing strains and could contribute to the spread of resistance genes from farm-derived Salmonella to other bacterial species present in the human gut.
Collapse
Affiliation(s)
- Hiroaki Shigemura
- Division of Pathology and Microbiology, Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Eri Sakatsume
- Kotobiken Medical Laboratories, Inc., Fukushima, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Yoshiki Etoh
- Division of Pathology and Microbiology, Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Yuki Carle
- Division of Pathology and Microbiology, Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Shiro Mizumoto
- Department of Microbiology, Shizuoka Institute of Environment and Hygiene, Shizuoka, Japan
| | - Shinichiro Hirai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mari Matsui
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- School of Medical Technology, Faculty of Health Science, Gunma Paz University, Gunma, Japan
| | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Daisuke Onozuka
- Department of Preventive Medicine and Epidemiology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yasuo Inoshima
- Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
16
|
Detection of Antimicrobial Resistance Genes Associated with Carbapenem Resistance from the Whole-Genome Sequence of Acinetobacter baumannii Isolates from Malaysia. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:5021064. [PMID: 32318127 PMCID: PMC7154965 DOI: 10.1155/2020/5021064] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 12/20/2022]
Abstract
Background The spread of carbapenem-resistant A. baumannii (CrAb) is gaining worldwide attention. The spread of this pathogen is largely due to its ability to acquire various resistance genes of intrinsic and extrinsic origins that confer unpredictable susceptibility to β-lactams. The aim of this study was to analyze β-lactamase genetic compositions of CrAb in Malaysia. Methods Whole-genome sequencing (WGS) was carried out on 13 CrAb isolates from clinical samples in Malaysia from 2011 to 2016. Results Endotracheal aspirate was the dominant clinical sample source (n = 6), and only one isolate was obtained from wound swab. A total of 6 sequence types (STs) of the Oxford scheme were identified, including 4 reported STs and 2 novel STs. Eleven isolates were classified into clonal complex 92 (CC92/ICII), among which ST195 and ST208 were the most prevalent STs. All 13 CrAb isolates harbored multiple β-lactamase genes. blaOXA-23 (n = 13) and blaOXA-66 (n = 11) were the dominant carbapenemase gene families found in these isolates. All isolates harbor blaADC, blaOXA-51-like, and blaOXA-23-like genes. blaTEM (n = 7), blaNDM-1 (n = 3), blaCARB-8 (n = 1), and blaPER-3 (n = 1) are amongst other β-lactamase genes found in this study. ISAba1 was found upstream to blaOXA-23 (n = 13), blaOXA-66 (n = 1), and blaADC (n = 11). All blaNDM-1 isolates had ISAba125 (mobile genetic element) upstream to the genes. All isolates were positive for Tn2006/2008 and Tn2009 but were negative for Tn2007. Conclusion Most of the isolates were grouped under the CC92 clonal complex which belongs to international clonal lineage 2. These findings predict that carriage of carbapenem-resistant genes possibly constitutes the underlying basis of high level of international clone II prevalence. Therefore, molecular surveillance and antimicrobial stewardship are essential in implementing policies to prevent and control the spread of CrAb in hospital settings.
Collapse
|
17
|
Shen Y, Zhang R, Schwarz S, Wu C, Shen J, Walsh TR, Wang Y. Farm animals and aquaculture: significant reservoirs of mobile colistin resistance genes. Environ Microbiol 2020; 22:2469-2484. [PMID: 32114703 DOI: 10.1111/1462-2920.14961] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 12/19/2022]
Abstract
Colistin resistance has attracted substantial attention after colistin was considered as a last-resort drug for the treatment of infections caused by carbapenem-resistant and/or multidrug-resistant (MDR) Gram-negative bacteria in clinical settings. However, with the discovery of highly mobile colistin resistance (mcr) genes, colistin resistance has become an increasingly urgent issue worldwide. Despite many reviews, which summarized the prevalence, mechanisms, and structures of these genes in bacteria of human and animal origin, studies on the prevalence of mobile colistin resistance genes in aquaculture and their transmission between animals and humans remain scarce. Herein, we review recent reports on the prevalence of colistin resistance genes in animals, especially wildlife and aquaculture, and their possibility of transmission to humans via the food chain. This review also gives some insights into the routine surveillance, changing policy and replacement of polymyxins by polymyxin derivatives, molecular inhibitors, and traditional Chinese medicine to tackle colistin resistance.
Collapse
Affiliation(s)
- Yingbo Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rong Zhang
- The Second Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, 310009, China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany
| | - Congming Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Timothy R Walsh
- Department of Medical Microbiology and Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park Hospital, Cardiff, CF14 4XN, UK
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
18
|
Truncated Class 1 Integron Gene Cassette Arrays Contribute to Antimicrobial Resistance of Diarrheagenic Escherichia coli. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4908189. [PMID: 32090095 PMCID: PMC7013361 DOI: 10.1155/2020/4908189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/30/2019] [Indexed: 11/17/2022]
Abstract
Class 1 integrons (c1-integrons) are associated with multidrug resistance in diarrheagenic Escherichia coli (DEC). However, little is known about gene cassettes located within these c1-integrons, particularly truncated c1-integrons, in DEC strains. Therefore, the aims of the present study were to reveal the relationship between antimicrobial resistance and the presence of truncated c1-integrons in DEC isolates derived from human stool samples in Japan. A total of 162 human stool-derived DEC isolates from Japan were examined by antimicrobial susceptibility testing, PCR-based gene detection, and next-generation sequencing analyses. Results showed that 44.4% (12/27) of c1-integrons identified in the DEC isolates harbored only intI1 (an element of c1-integrons) and were truncated by IS26, Tn3, or IS1-group insertion sequences. No difference in the frequency of antimicrobial resistance was recorded between intact and truncated c1-integron-positive DEC isolates. Isolates containing intact/truncated c1-integrons, particularly enteroaggregative E. coli isolates, were resistant to a greater number of antimicrobials than isolates without c1-integrons. aadA and dfrA were the most prevalent antimicrobial resistance genes in the intact/truncated c1-integrons examined in this study. Therefore, gene cassettes located within these intact/truncated c1-integrons may only play a limited role in conferring antimicrobial resistance among DEC. However, DEC harboring truncated c1-integrons may be resistant to a greater number of antimicrobials than c1-integron-negative DEC, similar to strains harboring intact c1-integrons.
Collapse
|
19
|
Polymyxin Susceptibility Testing and Interpretive Breakpoints: Recommendations from the United States Committee on Antimicrobial Susceptibility Testing (USCAST). Antimicrob Agents Chemother 2020; 64:AAC.01495-19. [PMID: 31767718 DOI: 10.1128/aac.01495-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The polymyxins are important agents for carbapenem-resistant Gram-negative bacilli. The United States Committee on Antimicrobial Susceptibility Testing breakpoint recommendations for colistin and polymyxin B are that isolates of Pseudomonas aeruginosa, Acinetobacter baumannii, and Enterobacteriaceae are considered susceptible at MIC values of ≤2 mg/liter. These recommendations are contingent upon dosing and testing strategies that are described in this commentary. Importantly, these recommendations are not applicable to lower respiratory tract infections, for which we recommend no breakpoints. Furthermore, there is no breakpoint recommendation for polymyxin B for lower urinary tract infections.
Collapse
|
20
|
Shedko ED, Timoshina O, Azyzov IS. Molecular epidemiology of mcr gene group. CLINICAL MICROBIOLOGY AND ANTIMICROBIAL CHEMOTHERAPY 2020. [DOI: 10.36488/cmac.2020.4.287-300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Colistin and polymyxin B are the “last reserve” antimicrobials for the treatment of extensively drug-resistant Gram-negative bacterial infections. The rapidly increasing prevalence of polymyxin resistance mediated by the mcr gene localized on plasmid DNA currently poses a high epidemiological threat. In order to control a distribution of mcr genes, it is necessary to develop highly accurate, highly sensitive and easy-to-use diagnostic tools. This paper provides a review of the most relevant studies on the molecular epidemiology as well as current approaches to microbiological and molecular detection of mcr group genes.
Collapse
|
21
|
Clostridioides (Clostridium) Difficile in Food-Producing Animals, Horses and Household Pets: A Comprehensive Review. Microorganisms 2019; 7:microorganisms7120667. [PMID: 31835413 PMCID: PMC6955671 DOI: 10.3390/microorganisms7120667] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 02/06/2023] Open
Abstract
Clostridioides (Clostridium) difficile is ubiquitous in the environment and is also considered as a bacterium of great importance in diarrhea-associated disease for humans and different animal species. Food animals and household pets are frequently found positive for toxigenic C. difficile without exposing clinical signs of infection. Humans and animals share common C. difficile ribotypes (RTs) suggesting potential zoonotic transmission. However, the role of animals for the development of human infection due to C. difficile remains unclear. One major public health issue is the existence of asymptomatic animals that carry and shed the bacterium to the environment, and infect individuals or populations, directly or through the food chain. C. difficile ribotype 078 is frequently isolated from food animals and household pets as well as from their environment. Nevertheless, direct evidence for the transmission of this particular ribotype from animals to humans has never been established. This review will summarize the current available data on epidemiology, clinical presentations, risk factors and laboratory diagnosis of C. difficile infection in food animals and household pets, outline potential prevention and control strategies, and also describe the current evidence towards a zoonotic potential of C. difficile infection.
Collapse
|
22
|
Liu G, Ali T, Gao J, Ur Rahman S, Yu D, Barkema HW, Huo W, Xu S, Shi Y, Kastelic JP, Han B. Co-Occurrence of Plasmid-Mediated Colistin Resistance ( mcr-1) and Extended-Spectrum β-Lactamase Encoding Genes in Escherichia coli from Bovine Mastitic Milk in China. Microb Drug Resist 2019; 26:685-696. [PMID: 31755810 DOI: 10.1089/mdr.2019.0333] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Both mcr-1 phosphoethanolamine transferase enzymes and extended-spectrum β-lactamases (ESBLs) are the main plasmid-mediated mechanisms of resistance to colistin and third-generation cephalosporins, respectively, and currently considered a major concern to humans and food animals. Prevalence of mcr-1 gene in Escherichia coli from dairy cattle has rarely been reported. Our objective was to determine prevalence and characteristics of mcr-1 carrying E. coli isolated from clinical mastitis cases in large dairy farms (>500 cows) in 16 provinces of China. A total of 249 E. coli was isolated from 2,038 mastitic milk samples. Among these isolates, 2.0% (n = 5) and 19.7% (n = 49) were colistin resistant mcr-1-positive and ESBL-producing isolates, respectively. All mcr-1-positive isolates that produced ESBLs also carried the blaCTX-M-15 gene and belonged to phylogroup-A. Most mcr-1 and blaCTX-M-15 genes were located on conjugative plasmids (IncP and IncF, respectively) that were successfully transferred to transconjugants in conjugation experiments. All mcr-1-positive E. coli isolates were multidrug resistant, exhibiting resistance to common antimicrobials. Multilocus sequence typing of these mcr-1-carrying E. coli isolates revealed four sequence types, reflecting substantial diversity. Multilocus sequence analysis detected evolutionary connection of mcr-1 carrying isolates with our recently reported ESBL-producing E. coli isolates, raising concerns regarding fast dissemination between bacteria. To our knowledge, this was the first nation-wide report describing isolates of E. coli from mastitic milk samples collected on large dairy farms in China, carrying mcr-1 and blaCTX-M-15 genes on conjugative plasmids. We concluded that dairy cattle are a potential source of mcr-1-carrying and ESBL-producing E. coli.
Collapse
Affiliation(s)
- Gang Liu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Tariq Ali
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
- Center of Microbiology and Biotechnology, Veterinary Research Institute Peshawar, Peshawar, Pakistan
| | - Jian Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Sadeeq Ur Rahman
- College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Garden Campus, Mardan, Pakistan
| | - Dan Yu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Herman W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Wenlin Huo
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Siyu Xu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Yuxiang Shi
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, P.R. China
| | - John P Kastelic
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Bo Han
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| |
Collapse
|
23
|
Le-Vo HN, Tran PTB, Le L, Matsumoto Y, Motooka D, Nakamura S, Jones JW, Iida T, Cao V. Complex Class 1 Integron in a Clinical Escherichia coli Strain From Vietnam Carrying Both mcr-1 and bla NDM-1. Front Microbiol 2019; 10:2472. [PMID: 31736911 PMCID: PMC6834847 DOI: 10.3389/fmicb.2019.02472] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/15/2019] [Indexed: 11/13/2022] Open
Abstract
The co-production of MCR and carbapenemase in Enterobacteriaceae has been previously reported. Here, we describe a clinical strain of Escherichia coli from Vietnam carrying both mcr-1 and bla NDM-1. Whole-genome sequencing showed that the genome of this strain consists of a 4,975,832-bp chromosome and four plasmids. The mcr-1 and bla NDM-1 genes are located on IncI2 and IncA/C2-type plasmids, respectively. Genetic analysis revealed the presence of a multidrug-resistant region with the structure of a novel complex class 1 integron including a class 1 integron region bearing two 5' conserved segments and one 3' conserved segment and two complete structures of ISCR1. The complex integron contains aminoglycoside resistance genes aadA2, aadB, strA, strB, and aphA6, quinolone resistance gene qnrA1, extended-spectrum β-lactamase gene bla OXA- 4, and a Tn125-like transposon bearing bla NDM-1. In addition, the dfrA12-gcuF-aadA2-cmlA1-aadA1-qacH gene cassette array belonging to the sul3-type integron was also identified, but the region found downstream of the gene cassette array is the IS440-tet(M)-IS26 element instead of the sul3 gene. The results further support that Enterobacteriaceae isolates co-harboring mcr and bla NDM are widely being distributed. The structural characteristics of the complex integron reveal that ISCR1 elements play an important role in the mobilization of bla NDM-1 and the development of multidrug-resistant regions.
Collapse
Affiliation(s)
- Hong-Ngoc Le-Vo
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Phuong Thi-Bich Tran
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Lien Le
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Yuki Matsumoto
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - James W Jones
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Tetsuya Iida
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Van Cao
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| |
Collapse
|
24
|
Acquisition of mcr-1 and Cocarriage of Virulence Genes in Avian Pathogenic Escherichia coli Isolates from Municipal Wastewater Influents in Japan. Appl Environ Microbiol 2019; 85:AEM.01661-19. [PMID: 31492666 DOI: 10.1128/aem.01661-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 08/29/2019] [Indexed: 12/11/2022] Open
Abstract
This study focused on the detection of the plasmid-mediated mcr colistin resistance gene in Escherichia coli isolates from wastewater treatment plants (WWTPs). Seven influent samples were collected from three WWTPs in Nagano Prefecture, Japan, during August and December 2018. Colistin-resistant E. coli isolates were selected on colistin-supplemented CHROMagar ECC plates. mcr-1-positive isolates were subjected to whole-genome sequencing (WGS) analysis. From six influent samples, seven mcr-1-positive but extended-spectrum β-lactamase (ESBL)-negative isolates belonging to different genetic lineages, namely, B2-O25:H4-ST131-fimH22, B2-O2:H1-ST135-fimH2, B1-O8:H9-ST764-fimH32, B1-O23:H16-ST453-fimH31, A-O81:H27-ST10-fimH54, A-O16:H5-ST871-fimH25, and F-O11:H6-ST457-fimH145, were detected. The MICs of colistin for these isolates ranged from 4 to 16 mg/liter. The mcr-1 genes were located on plasmids belonging to IncX4 and IncI2 in five and two isolates, respectively. Four IncX4 plasmids with the same size (33,309 bp) showed high sequence similarity (4 single-nucleotide variations). The remaining one IncX4 plasmid, with a size of 33,858 bp, carried the mcr-1 gene with the single synonymous nucleic substitution T27C. Two IncI2 plasmids with sizes of 60,710 bp and 60,733 bp had high sequence similarity (99.9% identity; 100% query coverage). Two of five isolates carrying IncX4 plasmids and both of the isolates carrying IncI2 plasmids harbored ColV plasmids carrying virulence-associated genes of avian pathogenic E. coli (APEC). In addition, another isolate of the B2-O25:H4-ST131-fimH22 lineage had those APEC-associated virulence genes on its chromosome. In conclusion, mcr-1-positive E. coli environmental isolates were mostly characterized as positive for APEC-associated virulence genes. The copresence of those genes may suggest the existence of a common source in animals and/or their associated environments.IMPORTANCE Colistin is considered a last-line therapeutic option in severe infections due to multidrug-resistant Gram-negative bacteria, in particular carbapenemase-producing Enterobacteriaceae and multidrug-resistant Acinetobacter baumannii An increasing prevalence of mcr genes in diverse Enterobacteriaceae species, mainly Escherichia coli and Klebsiella pneumoniae from humans and food animals, has become a significant concern to public health all over the world. In Japan, mcr genes have so far been detected in food animals, raw meat, wastewater, and human clinical samples. This study reports the copresence of mcr-1 and avian pathogenic E. coli (APEC)-associated virulence genes in five of seven E. coli isolates recovered from aquatic environments in Japan. Our study highlights the importance and urgency of action to reduce environmental contamination by mcr genes that may likely occur due to exposure to untreated wastewater through combined sewer overflow by recent unusual weather.
Collapse
|
25
|
Masuda K, Ooka T, Akita H, Hiratsuka T, Takao S, Fukada M, Inoue K, Honda M, Toda J, Sugitani W, Narimatsu H, Ishioka T, Hirai S, Sekizuka T, Kuroda M, Morita Y, Hayashi T, Kimura H, Oishi K, Ohnishi M, Fujimoto S, Murakami K. Epidemiological Aspects of Escherichia albertii Outbreaks in Japan and Genetic Characteristics of the Causative Pathogen. Foodborne Pathog Dis 2019; 17:144-150. [PMID: 31603704 DOI: 10.1089/fpd.2019.2654] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Zoonotic pathogen Escherichia albertii has been identified as the cause of several human disease outbreaks; however, factors such as the general symptoms and incubation period of E. albertii infection have yet to be defined. Therefore, we aimed to determine the unique aspects of E. albertii outbreaks in Japan and to examine the genetic characteristics of the causative pathogen. We studied all known E. albertii outbreaks that occurred in Japan up until 2015, which consisted of five confirmed outbreaks and one putative outbreak (Outbreaks 1-6). Outbreaks were re-examined based on personal communications between researchers in prefectural and municipal public health institutes, and through examination of any published study conducted at the time. Draft genome sequences of outbreak-associated E. albertii isolates were also generated. The most common symptom displayed by patients across the six episodes was watery diarrhea (>80%), followed by abdominal pain (50-84%) and fever (37.0-39.5°C) (26-44%). The estimated average incubation period of E. albertii infection was 12-24 h. We assumed that most of the outbreaks were foodborne or waterborne, with restaurant foods, restaurant water, and boxed lunches being the suspected transmission vehicles. Three of the six outbreak-associated E. albertii isolates possessed intact ETT2 regions, while the remaining isolates contained disrupted ETT2-encoding genes. Virulence gene screening revealed that more than half (44/70) of the tested genes were present in all 5 strains examined, and that each of the strains contained more than 1 gene from 14 out of the 21 groups of virulence genes examined in this study. The five E. albertii strains were classified into four of the five known phylogroups. Therefore, we determined that multiple E. albertii genotypes in Japan have the potential to cause outbreaks of diarrhea, abdominal pain, and/or fever following infection of a human host.
Collapse
Affiliation(s)
- Kanako Masuda
- Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, Hiroshima, Japan
| | - Tadasuke Ooka
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Hiroko Akita
- Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, Hiroshima, Japan
| | - Takahiro Hiratsuka
- Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, Hiroshima, Japan
| | - Shinichi Takao
- Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, Hiroshima, Japan
| | - Mami Fukada
- Hiroshima Prefectural Western Center for Public Health, Hiroshima, Japan
| | - Kaori Inoue
- Hiroshima Prefectural Western Center for Public Health, Hiroshima, Japan
| | - Mikiko Honda
- Fukuoka City Institute of Hygiene and the Environment, Fukuoka, Japan
| | - Junko Toda
- Kumamoto Prefectural Institute of Public-Health and Environmental Science, Kumamoto, Japan
| | - Wakana Sugitani
- Kumamoto City Environmental Research Institute, Kumamoto, Japan
| | - Hiroshi Narimatsu
- Oita Prefectural Institute of Health and the Environment, Oita, Japan
| | | | - Shinichiro Hirai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukio Morita
- Department of Food and Nutrition, Faculty of Home Economics, Tokyo Kasei University, Tokyo, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hirokazu Kimura
- School of Medical Technology, Faculty of Health Science, Gunma Paz University, Takasaki, Japan
| | - Kazunori Oishi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
26
|
Rozwandowicz M, Brouwer MSM, Fischer J, Wagenaar JA, Gonzalez-Zorn B, Guerra B, Mevius DJ, Hordijk J. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother 2019; 73:1121-1137. [PMID: 29370371 DOI: 10.1093/jac/dkx488] [Citation(s) in RCA: 495] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacterial antimicrobial resistance (AMR) is constantly evolving and horizontal gene transfer through plasmids plays a major role. The identification of plasmid characteristics and their association with different bacterial hosts provides crucial knowledge that is essential to understand the contribution of plasmids to the transmission of AMR determinants. Molecular identification of plasmid and strain genotypes elicits a distinction between spread of AMR genes by plasmids and dissemination of these genes by spread of bacterial clones. For this reason several methods are used to type the plasmids, e.g. PCR-based replicon typing (PBRT) or relaxase typing. Currently, there are 28 known plasmid types in Enterobacteriaceae distinguished by PBRT. Frequently reported plasmids [IncF, IncI, IncA/C, IncL (previously designated IncL/M), IncN and IncH] are the ones that bear the greatest variety of resistance genes. The purpose of this review is to provide an overview of all known AMR-related plasmid families in Enterobacteriaceae, the resistance genes they carry and their geographical distribution.
Collapse
Affiliation(s)
- M Rozwandowicz
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - M S M Brouwer
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Fischer
- Department of Biological Safety, Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - J A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - B Gonzalez-Zorn
- Department of Animal Health and VISAVET, Complutense University of Madrid, Madrid, Spain
| | - B Guerra
- Department of Biological Safety, Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - D J Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
27
|
Abstract
Polymyxins are important lipopeptide antibiotics that serve as the last-line defense against multidrug-resistant (MDR) Gram-negative bacterial infections. Worryingly, the clinical utility of polymyxins is currently facing a serious threat with the global dissemination of mcr, plasmid-mediated polymyxin resistance. The first plasmid-mediated polymyxin resistance gene, termed as mcr-1 was identified in China in November 2015. Following its discovery, isolates carrying mcr, mainly mcr-1 and less commonly mcr-2 to -7, have been reported across Asia, Africa, Europe, North America, South America and Oceania. This review covers the epidemiological, microbiological and genomics aspects of this emerging threat to global human health. The mcr has been identified in various species of Gram-negative bacteria including Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Salmonella enterica, Cronobacter sakazakii, Kluyvera ascorbata, Shigella sonnei, Citrobacter freundii, Citrobacter braakii, Raoultella ornithinolytica, Proteus mirabilis, Aeromonas, Moraxella and Enterobacter species from animal, meat, food product, environment and human sources. More alarmingly is the detection of mcr in extended-spectrum-β-lactamases- and carbapenemases-producing bacteria. The mcr can be carried by different plasmids, demonstrating the high diversity of mcr plasmid reservoirs. Our review analyses the current knowledge on the emergence of mcr-mediated polymyxin resistance.
Collapse
Affiliation(s)
- Sue C Nang
- a Department of Microbiology, Monash Biomedicine Discovery Institute , Monash University , Melbourne , Australia
| | - Jian Li
- a Department of Microbiology, Monash Biomedicine Discovery Institute , Monash University , Melbourne , Australia
| | - Tony Velkov
- b Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences , The University of Melbourne , Parkville , Australia
| |
Collapse
|
28
|
Merida-Vieyra J, De Colsa-Ranero A, Arzate-Barbosa P, Arias-de la Garza E, Méndez-Tenorio A, Murcia-Garzón J, Aquino-Andrade A. First clinical isolate of Escherichia coli harboring mcr-1 gene in Mexico. PLoS One 2019; 14:e0214648. [PMID: 30947268 PMCID: PMC6448934 DOI: 10.1371/journal.pone.0214648] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/17/2019] [Indexed: 11/19/2022] Open
Abstract
Our aim in this report was to describe the characteristics of the first clinical isolate of Escherichia coli (EC-PAG-733) harboring the mcr-1 gene found in Mexico. This isolate was obtained from a fecal sample from a young child with an oncological condition. We obtained the whole-genome sequence using next-generation sequencing and analyzed the sequence by bioinformatics tools. EC-PAG-733 was resistant to third- and fourth-generation cephalosporins and was susceptible to all carbapenems and amikacin; it was also resistant to ciprofloxacin, levofloxacin, gentamicin and colistin at a minimum inhibitory concentration (MIC) of 4 μg/mL. This isolate was classified as O11:H25-ST457. EC-PAG-733 harbored an ESBL type CTX-M-55 as well as several virulence factors that have been associated with Enteroaggregative Escherichia coli (EAEC). The mcr-1 gene was located within an IncI2 plasmid. The results of this whole genome shotgun project were deposited in DDBJ/ENA/GenBank under the accession number QKXE00000000.
Collapse
Affiliation(s)
- Jocelin Merida-Vieyra
- Molecular Microbiology Laboratory, Instituto Nacional de Pediatria (National Institute of Pediatrics INP), Mexico City, Mexico
| | - Agustín De Colsa-Ranero
- Molecular Microbiology Laboratory, Instituto Nacional de Pediatria (National Institute of Pediatrics INP), Mexico City, Mexico.,Pediatric Infectious Diseases Department, INP, Mexico City, Mexico
| | | | | | - Alfonso Méndez-Tenorio
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional (National School of Biological Sciences, National Polytechnic Institute), Mexico City, Mexico
| | - Jazmin Murcia-Garzón
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional (National School of Biological Sciences, National Polytechnic Institute), Mexico City, Mexico
| | - Alejandra Aquino-Andrade
- Molecular Microbiology Laboratory, Instituto Nacional de Pediatria (National Institute of Pediatrics INP), Mexico City, Mexico
| |
Collapse
|
29
|
Abstract
There is broad consensus internationally that surveillance of the levels of antimicrobial resistance (AMR) occurring in various systems underpins strategies to address the issue. The key reasons for surveillance of resistance are to determine (i) the size of the problem, (ii) whether resistance is increasing, (iii) whether previously unknown types of resistance are emerging, (iv) whether a particular type of resistance is spreading, and (v) whether a particular type of resistance is associated with a particular outbreak. The implications of acquiring and utilizing this information need to be considered in the design of a surveillance system. AMR surveillance provides a foundation for assessing the burden of AMR and for providing the necessary evidence for developing efficient and effective control and prevention strategies. The codevelopment of AMR surveillance programs in humans and animals is essential, but there remain several key elements that make data comparisons between AMR monitoring programs, and between regions, difficult. Currently, AMR surveillance relies on uncomplicated in vitro antimicrobial susceptibility methods. However, the lack of harmonization across programs and the limitation of genetic information of AMR remain the major drawbacks of these phenotypic methods. The future of AMR surveillance is moving toward genotypic detection, and molecular analysis methods are expected to yield a wealth of information. However, the expectation that these molecular techniques will surpass phenotypic susceptibility testing in routine diagnosis and monitoring of AMR remains a distant reality, and phenotypic testing remains necessary in the detection of emerging resistant bacteria, new resistance mechanisms, and trends of AMR.
Collapse
|
30
|
Bardet L, Rolain JM. Development of New Tools to Detect Colistin-Resistance among Enterobacteriaceae Strains. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2018; 2018:3095249. [PMID: 30631384 PMCID: PMC6305056 DOI: 10.1155/2018/3095249] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/11/2018] [Indexed: 12/27/2022]
Abstract
The recent discovery of the plasmid-mediated mcr-1 gene conferring resistance to colistin is of clinical concern. The worldwide screening of this resistance mechanism among samples of different origins has highlighted the urgent need to improve the detection of colistin-resistant isolates in clinical microbiology laboratories. Currently, phenotypic methods used to detect colistin resistance are not necessarily suitable as the main characteristic of the mcr genes is the low level of resistance that they confer, close to the clinical breakpoint recommended jointly by the CLSI and EUCAST expert systems (S ≤ 2 mg/L and R > 2 mg/L). In this context, susceptibility testing recommendations for polymyxins have evolved and are becoming difficult to implement in routine laboratory work. The large number of mechanisms and genes involved in colistin resistance limits the access to rapid detection by molecular biology. It is therefore necessary to implement well-defined protocols using specific tools to detect all colistin-resistant bacteria. This review aims to summarize the current clinical microbiology diagnosis techniques and their ability to detect all colistin resistance mechanisms and describe new tools specifically developed to assess plasmid-mediated colistin resistance. Phenotyping, susceptibility testing, and genotyping methods are presented, including an update on recent studies related to the development of specific techniques.
Collapse
Affiliation(s)
- Lucie Bardet
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| |
Collapse
|
31
|
Nishino Y, Shimojima Y, Suzuki Y, Ida M, Fukui R, Kuroda S, Hirai A, Sadamasu K. Detection of the mcr-1 gene in colistin-resistant Escherichia coli from retail meat in Japan. Microbiol Immunol 2018; 61:554-557. [PMID: 29052266 DOI: 10.1111/1348-0421.12549] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/25/2017] [Accepted: 10/05/2017] [Indexed: 11/28/2022]
Abstract
In this study, the presence of the mcr-1 gene in Escherichia coli from retail meat in Japan was investigated. Nine E. coli isolates (eight from chickens and one from pork) carried the mcr-1 gene on the plasmid. In six isolates from domestic chickens, mcr-1 was located on the IncI2 plasmid, which is approximately 60 kb in size. In the remaining three isolates from imported chicken and pork, mcr-1 was located on the IncX4 plasmid (30 kb).
Collapse
Affiliation(s)
- Yukari Nishino
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Yukako Shimojima
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Yasunori Suzuki
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Miki Ida
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Rie Fukui
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Sumiyo Kuroda
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Akihiko Hirai
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| |
Collapse
|
32
|
Liu H, Zhu B, Liang B, Xu X, Qiu S, Jia L, Li P, Yang L, Li Y, Xiang Y, Xie J, Wang L, Yang C, Sun Y, Song H. A Novel mcr-1 Variant Carried by an IncI2-Type Plasmid Identified From a Multidrug Resistant Enterotoxigenic Escherichia coli. Front Microbiol 2018; 9:815. [PMID: 29922243 PMCID: PMC5996929 DOI: 10.3389/fmicb.2018.00815] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 04/10/2018] [Indexed: 01/09/2023] Open
Abstract
In this study, we discovered a novel mobilized colistin resistance (mcr-1) gene variant, named mcr-1.9, which was identified in a colistin-resistant enterotoxigenic Escherichia coli (ETEC) strain from a clinical diarrhea case. The mcr-1.9 gene differs from mcr-1 at position 1036 due to a single nucleotide polymorphism (G→A), which results in an aspartic acid residue being replaced by an asparagine residue (Asp346→Asn) in the MCR-1 protein sequence. Antimicrobial susceptibility testing showed that the mcr-1.9-harboring ETEC strain is resistant to colistin at a minimum inhibitory concentration of 4 μg/ml. Plasmid profiling and conjugation experiments also suggest that the mcr-1.9 variant can be successfully transferred into the E. coli strain J53, indicating that the gene is located on a transferable plasmid. Bioinformatics analysis of data obtained from genome sequencing indicates that the mcr-1.9 gene is located on a 64,005 bp plasmid which has been named pEC26. This plasmid was found to have high similarity to the mcr-1-bearing IncI2-type plasmids pWF-5-19C (99% identity and 99% coverage) and pmcr1-IncI2 (99% identity and 98% coverage). The mcr-1.9-harboring ETEC also shows multidrug resistance to nine classes of antibiotics, and contains several virulence and antimicrobial-resistance genes suggested by the genome sequence analysis. Our report is the first to identify a new mcr-1 variant in an ETEC isolated from a human fecal sample, raising concerns about the existence of more such variants in human intestinal flora. Therefore, we believe that an undertaking to identify new mcr-1 variants in the bacterial communities of human intestines is of utmost importance, and that measures need to be taken to control the spread of mcr-1 and its variants in human intestinal microflora.
Collapse
Affiliation(s)
- Hongbo Liu
- College of Military Medicine, Academy of Military Medical Sciences, Beijing, China.,Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| | - Binghua Zhu
- College of Military Medicine, Academy of Military Medical Sciences, Beijing, China.,Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| | - Beibei Liang
- College of Military Medicine, Academy of Military Medical Sciences, Beijing, China.,Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| | - Xuebin Xu
- Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Shaofu Qiu
- Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| | - Leili Jia
- Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| | - Peng Li
- Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| | - Lang Yang
- College of Military Medicine, Academy of Military Medical Sciences, Beijing, China.,Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| | - Yongrui Li
- Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| | - Ying Xiang
- College of Military Medicine, Academy of Military Medical Sciences, Beijing, China.,Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| | - Jing Xie
- Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| | - Ligui Wang
- Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| | - Chaojie Yang
- Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| | - Yansong Sun
- College of Military Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Hongbin Song
- College of Military Medicine, Academy of Military Medical Sciences, Beijing, China.,Institute of Disease Control and Prevention, People's Liberation Army, Beijing, China
| |
Collapse
|
33
|
Plasmid-mediated colistin resistance in animals: current status and future directions. Anim Health Res Rev 2018; 18:136-152. [DOI: 10.1017/s1466252317000111] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
AbstractColistin, a peptide antibiotic belonging to the polymyxin family, is one of the last effective drugs for the treatment of multidrug resistant Gram-negative infections. Recent discovery of a novel mobile colistin resistance gene,mcr-1, from people and food animals has caused a significant public health concern and drawn worldwide attention. Extensive usage of colistin in food animals has been proposed as a major driving force for the emergence and transmission ofmcr-1; thus, there is a worldwide trend to limit colistin usage in animal production. However, despite lack of colistin usage in food animals in the USA,mcr-1-positiveEscherichia coliisolates were still isolated from swine. In this paper, we provided an overview of colistin usage and epidemiology ofmcr-1in food animals, and summarized the current status of mechanistic and evolutionary studies of the plasmid-mediated colistin resistance. Based on published information, we further discussed several non-colistin usage risk factors that may contribute to the persistence, transmission, and emergence of colistin resistance in an animal production system. Filling the knowledge gaps identified in this review is critical for risk assessment and risk management of colistin resistance, which will facilitate proactive and effective strategies to mitigate colistin resistance in future animal production systems.
Collapse
|
34
|
Ellem JA, Ginn AN, Chen SCA, Ferguson J, Partridge SR, Iredell JR. Locally Acquired mcr-1 in Escherichia coli, Australia, 2011 and 2013. Emerg Infect Dis 2018. [PMID: 28628439 PMCID: PMC5512495 DOI: 10.3201/eid2307.161638] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
We identified discrete importation events of the mcr-1 gene on incompatibility group IncI2 plasmids in Escherichia coli isolated from patients in New South Wales, Australia, in 2011 and 2013. mcr-1 is present in a small minority of colistin-resistant Enterobacteriaceae and appears not to be established locally.
Collapse
|
35
|
Kusumoto M, Ogura Y, Gotoh Y, Iwata T, Hayashi T, Akiba M. Colistin-Resistant mcr-1-Positive Pathogenic Escherichia coli in Swine, Japan, 2007-2014. Emerg Infect Dis 2018; 22:1315-7. [PMID: 27314277 PMCID: PMC4918142 DOI: 10.3201/eid2207.160234] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
36
|
Wei P, Song G, Shi M, Zhou Y, Liu Y, Lei J, Chen P, Yin L. Substrate analog interaction with MCR-1 offers insight into the rising threat of the plasmid-mediated transferable colistin resistance. FASEB J 2018; 32:1085-1098. [PMID: 29079699 DOI: 10.1096/fj.201700705r] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Colistin is considered a last-resort antibiotic against most gram-negative bacteria. Recent discoveries of a plasmid-mediated, transferable mobilized colistin-resistance gene ( mcr-1) on all continents have heralded the imminent emergence of pan-drug-resistant superbacteria. The inner-membrane protein MCR-1 can catalyze the transfer of phosphoethanolamine (PEA) to lipid A, resulting in colistin resistance. However, little is known about the mechanism, and few drugs exist to address this issue. We present crystal structures revealing the MCR-1 catalytic domain (cMCR-1) as a monozinc metalloprotein with ethanolamine (ETA) and d-glucose, respectively, thus highlighting 2 possible substrate-binding pockets in the MCR-1-catalyzed PEA transfer reaction. Mutation of the residues involved in ETA and d-glucose binding impairs colistin resistance in recombinant Escherichia coli containing full-length MCR-1. Partial analogs of the substrate are used for cocrystallization with cMCR-1, providing valuable information about the family of PEA transferases. One of the analogs, ETA, causes clear inhibition of polymyxin B resistance, highlighting its potential for drug development. These data demonstrate the crucial role of the PEA- and lipid A-binding pockets and provide novel insights into the structure-based mechanisms, important drug-target hot spots, and a drug template for further drug development to combat the urgent, rising threat of MCR-1-mediated antibiotic resistance.-Wei, P., Song, G., Shi, M., Zhou, Y., Liu, Y., Lei, J., Chen, P., Yin, L. Substrate analog interaction with MCR-1 offers insight into the rising threat of the plasmid-mediated transferable colistin resistance.
Collapse
Affiliation(s)
- Pengcheng Wei
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Guangji Song
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mengyang Shi
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yafei Zhou
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Liu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jun Lei
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Peng Chen
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lei Yin
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| |
Collapse
|
37
|
Ishii Y, Aoki K, Endo S, Kiyota H, Aoyagi T, Kaku M, Bonomo RA, Tateda K. Spread of mcr-1.5 in the community: an emerging threat. Int J Antimicrob Agents 2017; 51:161-162. [PMID: 29127048 DOI: 10.1016/j.ijantimicag.2017.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 10/28/2017] [Indexed: 10/18/2022]
Affiliation(s)
- Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16 Omori-nishi, Ota-ku, Tokyo 1438540, Japan.
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16 Omori-nishi, Ota-ku, Tokyo 1438540, Japan
| | - Shiro Endo
- Department of Infection Control and Laboratory Diagnostics, Internal Medicine, Tohoku University Graduate School of Medicine, 1-1 Seiryoumachi, Aoba-ku, Sendai, Miyagi 9808574, Japan
| | - Hiroshi Kiyota
- Department of Urology, The Jikei University Katsushika Medical Center, 6-41-2 Aoto, Katsushika-ku, Tokyo 1258506, Japan
| | - Tetsuji Aoyagi
- Department of Infection Control and Laboratory Diagnostics, Internal Medicine, Tohoku University Graduate School of Medicine, 1-1 Seiryoumachi, Aoba-ku, Sendai, Miyagi 9808574, Japan
| | - Mitsuo Kaku
- Department of Infection Control and Laboratory Diagnostics, Internal Medicine, Tohoku University Graduate School of Medicine, 1-1 Seiryoumachi, Aoba-ku, Sendai, Miyagi 9808574, Japan
| | - Robert A Bonomo
- Medical Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16 Omori-nishi, Ota-ku, Tokyo 1438540, Japan
| |
Collapse
|
38
|
Polymyxins: Antibacterial Activity, Susceptibility Testing, and Resistance Mechanisms Encoded by Plasmids or Chromosomes. Clin Microbiol Rev 2017; 30:557-596. [PMID: 28275006 DOI: 10.1128/cmr.00064-16] [Citation(s) in RCA: 889] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Polymyxins are well-established antibiotics that have recently regained significant interest as a consequence of the increasing incidence of infections due to multidrug-resistant Gram-negative bacteria. Colistin and polymyxin B are being seriously reconsidered as last-resort antibiotics in many areas where multidrug resistance is observed in clinical medicine. In parallel, the heavy use of polymyxins in veterinary medicine is currently being reconsidered due to increased reports of polymyxin-resistant bacteria. Susceptibility testing is challenging with polymyxins, and currently available techniques are presented here. Genotypic and phenotypic methods that provide relevant information for diagnostic laboratories are presented. This review also presents recent works in relation to recently identified mechanisms of polymyxin resistance, including chromosomally encoded resistance traits as well as the recently identified plasmid-encoded polymyxin resistance determinant MCR-1. Epidemiological features summarizing the current knowledge in that field are presented.
Collapse
|
39
|
Webb HE, Angulo FJ, Granier SA, Scott HM, Loneragan GH. Illustrative examples of probable transfer of resistance determinants from food animals to humans: Streptothricins, glycopeptides, and colistin. F1000Res 2017; 6:1805. [PMID: 29188021 PMCID: PMC5686510 DOI: 10.12688/f1000research.12777.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/15/2017] [Indexed: 12/24/2022] Open
Abstract
Use, overuse, and misuse of antimicrobials contributes to selection and dissemination of bacterial resistance determinants that may be transferred to humans and constitute a global public health concern. Because of the continued emergence and expansion of antimicrobial resistance, combined with the lack of novel antimicrobial agents, efforts are underway to preserve the efficacy of current available life-saving antimicrobials in humans. As a result, uses of medically important antimicrobials in food animal production have generated debate and led to calls to reduce both antimicrobial use and the need for use. This manuscript, commissioned by the World Health Organization (WHO) to help inform the development of the WHO guidelines on the use of medically important antimicrobials in food animals, includes three illustrations of antimicrobial use in food animal production that has contributed to the selection-and subsequent transfer-of resistance determinants from food animals to humans. Herein, antimicrobial use and the epidemiology of bacterial resistance are described for streptothricins, glycopeptides, and colistin. Taken together, these historical and current narratives reinforce the need for actions that will preserve the efficacy of antimicrobials.
Collapse
Affiliation(s)
- Hattie E. Webb
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Frederick J. Angulo
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Sophie A. Granier
- Laboratory for Food Safety, Anses, Université Paris-Est, Maisons-Alfort, F-94701, France
| | - H. Morgan Scott
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Guy H. Loneragan
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| |
Collapse
|
40
|
Tada T, Uechi K, Nakasone I, Shimada K, Nakamatsu M, Kirikae T, Fujita J. Emergence of a colistin-resistant Escherichia coli clinical isolate harboring mcr-1 in Japan. Int J Infect Dis 2017; 63:21-22. [PMID: 28780184 DOI: 10.1016/j.ijid.2017.07.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/24/2017] [Accepted: 07/26/2017] [Indexed: 12/01/2022] Open
Abstract
The mcr-1 is a gene encoding a phosphoethanolamine transferase, which confers resistance to colistin by transferring phosphoethanolamine to lipid A. We describe here the emergence of a colistin-resistant Escherichia coli clinical isolate harboring plasmid-mediated mcr-1 in Japan. The isolate belonged to ST5702 and is suspected to come from livestock and transmitted to human. This is the first report of a clinical isolate harboring mcr-1 in Japan.
Collapse
Affiliation(s)
- Tatsuya Tada
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan; Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kohei Uechi
- Division of Clinical Laboratory and Blood Transfusion, University Hospital of the Ryukyus, Okinawa, Japan; Department of Infectious Diseases, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Isamu Nakasone
- Control and Prevention of Infectious Disease, University Hospital of the Ryukyus, Okinawa, Japan
| | - Kayo Shimada
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masashi Nakamatsu
- Department of Infectious Diseases, Faculty of the Ryukyus, Okinawa, Japan
| | - Teruo Kirikae
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan; Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan.
| | - Jiro Fujita
- Department of Infectious Diseases, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| |
Collapse
|
41
|
Schürch AC, van Schaik W. Challenges and opportunities for whole-genome sequencing-based surveillance of antibiotic resistance. Ann N Y Acad Sci 2017; 1388:108-120. [PMID: 28134443 DOI: 10.1111/nyas.13310] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 12/13/2022]
Abstract
Infections caused by drug-resistant bacteria are increasingly reported across the planet, and drug-resistant bacteria are recognized to be a major threat to public health and modern medicine. In this review, we discuss how whole-genome sequencing (WGS)-based approaches can contribute to the surveillance of the emergence and spread of antibiotic resistance. We outline the characteristics of sequencing technologies that are currently most used for WGS (Illumina short-read technologies and the long-read sequencing platforms developed by Pacific Biosciences and Oxford Nanopore). The challenges posed by the analysis of sequencing data sets for antimicrobial-resistance determinants and the solutions offered by modern bioinformatics tools are discussed. Finally, we illustrate the power of WGS-based surveillance of antimicrobial resistance by summarizing recent studies on the spread of the multidrug-resistant opportunistic pathogen Klebsiella pneumoniae and the transferable colistin-resistance gene mcr-1, in which high-throughput WGS analyses played essential roles. The implementation of WGS for surveillance of antibiotic-resistant bacteria is technically feasible and cost effective and provides actionable results with reference to infection control. Consequently, the time has come for laboratories to implement routine genome sequencing as part of their surveillance programs for antibiotic-resistant bacteria.
Collapse
Affiliation(s)
- Anita C Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| |
Collapse
|
42
|
Ohsaki Y, Hayashi W, Saito S, Osaka S, Taniguchi Y, Koide S, Kawamura K, Nagano Y, Arakawa Y, Nagano N. First Detection of an Escherichia coli Strain Harboring the mcr-1 Gene in Retail Domestic Chicken Meat in Japan. Jpn J Infect Dis 2017; 70:590-592. [PMID: 28674313 DOI: 10.7883/yoken.jjid.2016.572] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Global spread of the plasmid-mediated colistin resistance gene, mcr-1 poses a challenge to public health because colistin is the last-line-of-defense against severe infections of multidrug-resistant Gram-negative bacteria. In Japan, a few studies have reported the prevalence of mcr-1 among food animal-derived Escherichia coli isolates, but the prevalence of mcr-1 in retail meats is not well known. We report here the first detection of mcr-1 in retail chicken meat. A total of 70 extended-spectrum beta-lactamase-producing E. coli isolates, recovered from retail chicken meats between August 2015 and June 2016, were screened for mcr-1. We found 1 CTX-M-1 beta-lactamase-producing E. coli isolate belonging to ST1684, phylogroup A. The mcr-1 gene was not located on an IncI1 plasmid encoding the blaCTX-M-1 gene. However, whole plasmid sequencing revealed that mcr-1 was located on an IncI2 plasmid. The sequences of the nikB-mcr-1-pap2-ydfA-topB region of the IncI2 plasmid in this study was almost identical to that of the previously described IncI2 plasmid, pECJS-61-63 present in E. coli isolated from pig feces in China, except for containing a synonymous mutation in the mcr-1 gene. Plasmid carrying the mcr-1 gene have not yet been identified in human isolates in Japan. Thus, strict monitoring or surveillance of colistin resistance among Gram-negative bacteria recovered from retail meat of food animals under colistin pressure, and humans, is crucial.
Collapse
Affiliation(s)
- Yusuke Ohsaki
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine
| | - Wataru Hayashi
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine
| | - Satomi Saito
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine
| | - Shunsuke Osaka
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine
| | - Yui Taniguchi
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine
| | - Shota Koide
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine
| | - Kumiko Kawamura
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine
| | - Yukiko Nagano
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Noriyuki Nagano
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine
| |
Collapse
|
43
|
MCR-1.6, a New MCR Variant Carried by an IncP Plasmid in a Colistin-Resistant Salmonella enterica Serovar Typhimurium Isolate from a Healthy Individual. Antimicrob Agents Chemother 2017; 61:AAC.02632-16. [PMID: 28264851 DOI: 10.1128/aac.02632-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/20/2017] [Indexed: 11/20/2022] Open
Abstract
In this study, we report a novel mcr-1 gene variant, named mcr-1.6, carried by an IncP plasmid in a colistin-resistant Salmonella enterica serovar Typhimurium isolate from a healthy person. Compared with mcr-1, the mcr-1.6 gene contains two single-nucleotide polymorphisms, one of which results in an arginine to histidine variation (Arg536→His). The plasmid carrying the mcr-1.6 gene was designated pMCR1.6_P053 and is similar to a recently discovered mcr-1-bearing plasmid found in Klebsiella pneumoniae.
Collapse
|
44
|
Sekizuka T, Kawanishi M, Ohnishi M, Shima A, Kato K, Yamashita A, Matsui M, Suzuki S, Kuroda M. Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids. Sci Rep 2017; 7:928. [PMID: 28424528 PMCID: PMC5430464 DOI: 10.1038/s41598-017-01082-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/20/2017] [Indexed: 12/30/2022] Open
Abstract
A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing. The sequences assembled using only SMRT sequencing contained misassembled regions in the shufflon. A hybrid analysis using SMRT and Illumina sequencing resolved the misassembled region and revealed that the three IncI2 plasmids, excluding the shufflon region, were highly conserved. Moreover, the abundance ratio of whole-shufflon structures could be determined by quantitative structural variation analysis of the SMRT data, suggesting that a remarkable heterogeneity of whole-shufflon structural variations exists in IncI2 plasmids. These findings indicate that remarkable rearrangement regions should be validated using both long-read and short-read sequencing data and that the structural variation of PilV in the shufflon might be closely related to phenotypic heterogeneity of plasmid-mediated transconjugation involved in horizontal gene transfer even in bacterial clonal populations.
Collapse
Affiliation(s)
- Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjyuku-ku, Tokyo, 162-8640, Japan.
| | - Michiko Kawanishi
- Assay Division II, Bacterial Assay Section, National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, 1-15-1 Tokura, Kokubunji-shi, 185-8511, Tokyo, Japan
| | - Mamoru Ohnishi
- Ohnishi Laboratory of Veterinary Microbiology, 10-3-3 Nishirokujyouminami, Shibetsugunnakashibetsu-cho, 086-1106, Hokkaido, Japan
| | - Ayaka Shima
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Kengo Kato
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjyuku-ku, Tokyo, 162-8640, Japan
| | - Akifumi Yamashita
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjyuku-ku, Tokyo, 162-8640, Japan
| | - Mari Matsui
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Satowa Suzuki
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjyuku-ku, Tokyo, 162-8640, Japan
| |
Collapse
|
45
|
Chen X, Zhao X, Che J, Xiong Y, Xu Y, Zhang L, Lan R, Xia L, Walsh TR, Xu J, Lu J, Li J. Detection and dissemination of the colistin resistance gene, mcr-1, from isolates and faecal samples in China. J Med Microbiol 2017; 66:119-125. [PMID: 28056227 DOI: 10.1099/jmm.0.000425] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE A recently identified colistin resistance gene, mcr-1, has been reported in many countries. In this study, we established a new real-time PCR method to detect it. METHODOLOGY We used a real-time PCR method to detect the mcr-1 gene in a variety of isolates and faecal samples from 20 provinces and municipal cities in China. RESULTS Of the 2330 isolates (from 10 species) screened, 54 (2.3 %) isolates were positive for mcr-1. All of the mcr-1-positive isolates that were identified belonged to Escherichia coli strains, among which 9, 1, and 44 were identified as enteropathogenic E. coli, enteroadherent E. coli, and non-pathogenic E. coli, respectively. The majority of the mcr-1-positive isolates were obtained from farm animals from eight provinces and municipal cities across China. A total of 337 faecal samples, including 229 human and 108 pet animal faecal samples, were also screened for the mcr-1 gene. Of the 337 samples analyzed, six and eight human and pet animal faecal samples were positive for the mcr-1 gene, respectively. CONCLUSION The data demonstrate that the mcr-1 gene is highly prevalent in human and animal populations in China. This occurrence suggests that active surveillance of the mcr-1 gene is imperative in curtailing its spread.
Collapse
Affiliation(s)
- Xia Chen
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Xiaofei Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Jie Che
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Yanmei Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Lifeng Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Lining Xia
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, PR China
| | - Timothy R Walsh
- Department of Medical Microbiology, School of Medicine, Cardiff University, Cardiff, UK
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Jinxing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Juan Li
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| |
Collapse
|
46
|
A Phage-Like IncY Plasmid Carrying the mcr-1 Gene in Escherichia coli from a Pig Farm in China. Antimicrob Agents Chemother 2017; 61:AAC.02035-16. [PMID: 28031198 DOI: 10.1128/aac.02035-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/14/2016] [Indexed: 12/17/2022] Open
Abstract
We report here a new type of plasmid that carries the mcr-1 gene, the pMCR-1-P3 plasmid, harbored in an Escherichia coli strain isolated from a pig farm in China. pMCR-1-P3 belongs to the IncY incompatibility group and is a phage-like plasmid that contains a large portion of phage-related sequences. The backbone of this plasmid is different from that of other mcr-1-carrying plasmids reported previously.
Collapse
|
47
|
High Incidence of Escherichia coli Strains Coharboring mcr-1 and blaNDM from Chickens. Antimicrob Agents Chemother 2017; 61:AAC.02347-16. [PMID: 28069644 DOI: 10.1128/aac.02347-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/30/2016] [Indexed: 12/25/2022] Open
Abstract
This study investigated the characteristics of Escherichia coli isolates carrying mcr-1-blaNDM from a chicken farm in China. Of the 78 E. coli isolates, 21 clonally unrelated isolates carried mcr-1-blaNDM Diverse IncI2 plasmids disseminated mcr-1, while the dissemination of blaNDM was mediated by diverse IncB/O plasmids. More striking was the colocalization of resistance genes mcr-1 and blaNDM-4 in an IncHI2/ST3 plasmid, which might pose a great challenge for public health.
Collapse
|
48
|
Jeannot K, Bolard A, Plésiat P. Resistance to polymyxins in Gram-negative organisms. Int J Antimicrob Agents 2017; 49:526-535. [PMID: 28163137 DOI: 10.1016/j.ijantimicag.2016.11.029] [Citation(s) in RCA: 245] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/10/2016] [Accepted: 11/25/2016] [Indexed: 12/30/2022]
Abstract
Polymyxins have recently been re-introduced into the therapeutic arsenal to combat infections caused by multidrug-resistant Gram-negative bacteria. However, the emergence of strains resistant to these last-resort drugs is becoming a critical issue in a growing number of countries. Both intrinsic and transferable mechanisms of polymyxin resistance have been characterised. These mechanisms as well as the epidemiological data regarding four relevant bacterial pathogens (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa) are considered in this review. A special focus is made on plasmid-mediated resistance and the spread of mcr genes.
Collapse
Affiliation(s)
- Katy Jeannot
- Laboratoire de bactériologie, Centre national de référence (CNR) de la résistance aux antibiotiques, Centre hospitalier universitaire (CHRU) de Besançon, boulevard Fleming, 25000 Besançon, France.
| | - Arnaud Bolard
- Laboratoire de bactériologie, Centre national de référence (CNR) de la résistance aux antibiotiques, Centre hospitalier universitaire (CHRU) de Besançon, boulevard Fleming, 25000 Besançon, France
| | - Patrick Plésiat
- Laboratoire de bactériologie, Centre national de référence (CNR) de la résistance aux antibiotiques, Centre hospitalier universitaire (CHRU) de Besançon, boulevard Fleming, 25000 Besançon, France
| |
Collapse
|
49
|
Emergence of Colistin Resistance Gene mcr-1 in Cronobacter sakazakii Producing NDM-9 and in Escherichia coli from the Same Animal. Antimicrob Agents Chemother 2017; 61:AAC.01444-16. [PMID: 27855074 DOI: 10.1128/aac.01444-16] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/28/2016] [Indexed: 11/20/2022] Open
Abstract
We report the presence of mcr-1 in Escherichia coli and carbapenem-resistant Cronobacter sakazakii from the same diseased chicken. The mcr-1 gene linked with ISApl1 was located on two different IncI2 plasmids, including one multidrug plasmid in E. coli, whereas fosA3-blaNDM-9 was on an IncB/O plasmid in C. sakazakii The development of the fosA3-blaNDM-9 resistance region was mediated by IS26 The colocation of mcr-1 or blaNDM-9 with other resistance genes will accelerate the dissemination of the two genes.
Collapse
|
50
|
IncP Plasmid Carrying Colistin Resistance Gene mcr-1 in Klebsiella pneumoniae from Hospital Sewage. Antimicrob Agents Chemother 2017; 61:AAC.02229-16. [PMID: 27895009 DOI: 10.1128/aac.02229-16] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 11/18/2016] [Indexed: 02/05/2023] Open
Abstract
A Klebsiella pneumoniae strain of sequence type 313 (ST313) recovered from hospital sewage was found carrying the plasmid-borne colistin resistance gene mcr-1, which was bracketed by two copies of the insertion sequence ISApl1 on a 57-kb self-transmissible IncP-type plasmid of a new IncP-1 clade. The carriage of mcr-1 on a self-transmissible broad-host-range plasmid highlights that mcr-1 has the potential to spread beyond the Enterobacteriaceae family.
Collapse
|