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Muñoz-Gutiérrez I, Cantu L, Shanahan J, Girguis M, de la Cruz M, Mota-Bravo L. Cryptic environmental conjugative plasmid recruits a novel hybrid transposon resulting in a new plasmid with higher dispersion potential. mSphere 2024; 9:e0025224. [PMID: 38771049 DOI: 10.1128/msphere.00252-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 05/22/2024] Open
Abstract
Cryptic conjugative plasmids lack antibiotic-resistance genes (ARGs). These plasmids can capture ARGs from the vast pool of the environmental metagenome, but the mechanism to recruit ARGs remains to be elucidated. To investigate the recruitment of ARGs by a cryptic plasmid, we sequenced and conducted mating experiments with Escherichia coli SW4848 (collected from a lake) that has a cryptic IncX (IncX4) plasmid and an IncF (IncFII/IncFIIB) plasmid with five genes that confer resistance to aminoglycosides (strA and strB), sulfonamides (sul2), tetracycline [tet(A)], and trimethoprim (dfrA5). In a conjugation experiment, a novel hybrid Tn21/Tn1721 transposon of 22,570 bp (designated Tn7714) carrying the five ARG mobilized spontaneously from the IncF plasmid to the cryptic IncX plasmid. The IncF plasmid was found to be conjugative when it was electroporated into E. coli DH10B (without the IncX plasmid). Two parallel conjugations with the IncF and the new IncX (carrying the novel Tn7714 transposon) plasmids in two separate E. coli DH10B as donors and E. coli J53 as the recipient revealed that the conjugation rate of the new IncX plasmid (with the novel Tn7714 transposon and five ARGs) is more than two orders of magnitude larger than the IncF plasmid. For the first time, this study shows experimental evidence that cryptic environmental plasmids can capture and transfer transposons with ARGs to other bacteria, creating novel multidrug-resistant conjugative plasmids with higher dispersion potential. IMPORTANCE Cryptic conjugative plasmids are extrachromosomal DNA molecules without antibiotic-resistance genes (ARGs). Environmental bacteria carrying cryptic plasmids with a high conjugation rate threaten public health because they can capture clinically relevant ARGs and rapidly spread them to pathogenic bacteria. However, the mechanism to recruit ARG by cryptic conjugative plasmids in environmental bacteria has not been observed experimentally. Here, we document the first translocation of a transposon with multiple clinically relevant ARGs to a cryptic environmental conjugative plasmid. The new multidrug-resistant conjugative plasmid has a conjugation rate that is two orders of magnitude higher than the original plasmid that carries the ARG (i.e., the new plasmid from the environment can spread ARG more than two orders of magnitude faster). Our work illustrates the importance of studying the mobilization of ARGs in environmental bacteria. It sheds light on how cryptic conjugative plasmids recruit ARGs, a phenomenon at the root of the antibiotic crisis.
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Affiliation(s)
- Iván Muñoz-Gutiérrez
- School of Biological Sciences, University of California, Irvine, California, USA
| | - Luis Cantu
- School of Biological Sciences, University of California, Irvine, California, USA
| | - Jack Shanahan
- School of Biological Sciences, University of California, Irvine, California, USA
| | - Miray Girguis
- School of Biological Sciences, University of California, Irvine, California, USA
| | - Marlene de la Cruz
- School of Biological Sciences, University of California, Irvine, California, USA
| | - Luis Mota-Bravo
- School of Biological Sciences, University of California, Irvine, California, USA
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2
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Tan B, Zhang Q, Zhang L, Zhu Y, Zhang C. Naturally Occurring and Widespread Resistance to Bioactive Natural Products. ChemMedChem 2024; 19:e202300619. [PMID: 38103004 DOI: 10.1002/cmdc.202300619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 12/17/2023]
Abstract
Naturally occurring resistances diminish the effectiveness of antibiotics, and present significant challenges to human health. Human activities are usually considered as the main drivers of the dissemination of antibiotic resistance, however, the origin of the clinical antibiotic resistance can be traced to the environmental microbes, and the clinically relevant resistance determinants have already pre-existed in nature before the antibiotics come into clinic. In this concept, we present the naturally occurring and widespread resistance determinants recently discovered during the biosynthesis study of bioactive compounds. These widely prevalent resistances in environmental microbes, including antibiotic producers and non-producers, advance the understanding of the origin of resistance, and provide prediction for the clinically relevant resistance to aid in the rational design of more effective drug analogues to combat resistance.
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Affiliation(s)
- Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
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3
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Qi Q, Ghaly TM, Rajabal V, Gillings MR, Tetu SG. Dissecting molecular evolution of class 1 integron gene cassettes and identifying their bacterial hosts in suburban creeks via epicPCR. J Antimicrob Chemother 2024; 79:100-111. [PMID: 37962091 DOI: 10.1093/jac/dkad353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
OBJECTIVES Our study aimed to sequence class 1 integrons in uncultured environmental bacterial cells in freshwater from suburban creeks and uncover the taxonomy of their bacterial hosts. We also aimed to characterize integron gene cassettes with altered DNA sequences relative to those from databases or literature and identify key signatures of their molecular evolution. METHODS We applied a single-cell fusion PCR-based technique-emulsion, paired isolation and concatenation PCR (epicPCR)-to link class 1 integron gene cassette arrays to the phylogenetic markers of their bacterial hosts. The levels of streptomycin resistance conferred by the WT and altered aadA5 and aadA11 gene cassettes that encode aminoglycoside (3″) adenylyltransferases were experimentally quantified in an Escherichia coli host. RESULTS Class 1 integron gene cassette arrays were detected in Alphaproteobacteria and Gammaproteobacteria hosts. A subset of three gene cassettes displayed signatures of molecular evolution, namely the gain of a regulatory 5'-untranslated region (5'-UTR), the loss of attC recombination sites between adjacent gene cassettes, and the invasion of a 5'-UTR by an IS element. Notably, our experimental testing of a novel variant of the aadA11 gene cassette demonstrated that gaining the observed 5'-UTR contributed to a 3-fold increase in the MIC of streptomycin relative to the ancestral reference gene cassette in E. coli. CONCLUSIONS Dissecting the observed signatures of molecular evolution of class 1 integrons allowed us to explain their effects on antibiotic resistance phenotypes, while identifying their bacterial hosts enabled us to make better inferences on the likely origins of novel gene cassettes and IS that invade known gene cassettes.
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Affiliation(s)
- Qin Qi
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Timothy M Ghaly
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Vaheesan Rajabal
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Michael R Gillings
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
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4
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Lee JH, Kim NH, Jang KM, Jin H, Shin K, Jeong BC, Kim DW, Lee SH. Prioritization of Critical Factors for Surveillance of the Dissemination of Antibiotic Resistance in Pseudomonas aeruginosa: A Systematic Review. Int J Mol Sci 2023; 24:15209. [PMID: 37894890 PMCID: PMC10607276 DOI: 10.3390/ijms242015209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Pseudomonas aeruginosa is the primary opportunistic human pathogen responsible for a range of acute and chronic infections; it poses a significant threat to immunocompromised patients and is the leading cause of morbidity and mortality for nosocomial infections. Its high resistance to a diverse array of antimicrobial agents presents an urgent health concern. Among the mechanisms contributing to resistance in P. aeruginosa, the horizontal acquisition of antibiotic resistance genes (ARGs) via mobile genetic elements (MGEs) has gained recognition as a substantial concern in clinical settings, thus indicating that a comprehensive understanding of ARG dissemination within the species is strongly required for surveillance. Here, two approaches, including a systematic literature analysis and a genome database survey, were employed to gain insights into ARG dissemination. The genome database enabled scrutinizing of all the available sequence information and various attributes of P. aeruginosa isolates, thus providing an extensive understanding of ARG dissemination within the species. By integrating both approaches, with a primary focus on the genome database survey, mobile ARGs that were linked or correlated with MGEs, important sequence types (STs) carrying diverse ARGs, and MGEs responsible for ARG dissemination were identified as critical factors requiring strict surveillance. Although human isolates play a primary role in dissemination, the importance of animal and environmental isolates has also been suggested. In this study, 25 critical mobile ARGs, 45 critical STs, and associated MGEs involved in ARG dissemination within the species, are suggested as critical factors. Surveillance and management of these prioritized factors across the One Health sectors are essential to mitigate the emergence of multidrug-resistant (MDR) and extensively resistant (XDR) P. aeruginosa in clinical settings.
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Affiliation(s)
- Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Nam-Hoon Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Kyung-Min Jang
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Hyeonku Jin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Kyoungmin Shin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Dae-Wi Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
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Lund D, Coertze RD, Parras-Moltó M, Berglund F, Flach CF, Johnning A, Larsson DGJ, Kristiansson E. Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens. Commun Biol 2023; 6:812. [PMID: 37537271 PMCID: PMC10400643 DOI: 10.1038/s42003-023-05174-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023] Open
Abstract
Antibiotic resistance is a growing threat to human health, caused in part by pathogens accumulating antibiotic resistance genes (ARGs) through horizontal gene transfer. New ARGs are typically not recognized until they have become widely disseminated, which limits our ability to reduce their spread. In this study, we use large-scale computational screening of bacterial genomes to identify previously undiscovered mobile ARGs in pathogens. From ~1 million genomes, we predict 1,071,815 genes encoding 34,053 unique aminoglycoside-modifying enzymes (AMEs). These cluster into 7,612 families (<70% amino acid identity) of which 88 are previously described. Fifty new AME families are associated with mobile genetic elements and pathogenic hosts. From these, 24 of 28 experimentally tested AMEs confer resistance to aminoglycoside(s) in Escherichia coli, with 17 providing resistance above clinical breakpoints. This study greatly expands the range of clinically relevant aminoglycoside resistance determinants and demonstrates that computational methods enable early discovery of potentially emerging ARGs.
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Affiliation(s)
- David Lund
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Roelof Dirk Coertze
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marcos Parras-Moltó
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.
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Saturio S, Rey A, Samarra A, Collado MC, Suárez M, Mantecón L, Solís G, Gueimonde M, Arboleya S. Old Folks, Bad Boon: Antimicrobial Resistance in the Infant Gut Microbiome. Microorganisms 2023; 11:1907. [PMID: 37630467 PMCID: PMC10458625 DOI: 10.3390/microorganisms11081907] [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: 06/15/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
The development of the intestinal microbiome in the neonate starts, mainly, at birth, when the infant receives its founding microbial inoculum from the mother. This microbiome contains genes conferring resistance to antibiotics since these are found in some of the microorganisms present in the intestine. Similarly to microbiota composition, the possession of antibiotic resistance genes is affected by different perinatal factors. Moreover, antibiotics are the most used drugs in early life, and the use of antibiotics in pediatrics covers a wide variety of possibilities and treatment options. The disruption in the early microbiota caused by antibiotics may be of great relevance, not just because it may limit colonization by beneficial microorganisms and increase that of potential pathogens, but also because it may increase the levels of antibiotic resistance genes. The increase in antibiotic-resistant microorganisms is one of the major public health threats that humanity has to face and, therefore, understanding the factors that determine the development of the resistome in early life is of relevance. Recent advancements in sequencing technologies have enabled the study of the microbiota and the resistome at unprecedent levels. These aspects are discussed in this review as well as some potential interventions aimed at reducing the possession of resistance genes.
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Affiliation(s)
- Silvia Saturio
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.S.); (A.R.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
| | - Alejandra Rey
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.S.); (A.R.)
| | - Anna Samarra
- Institute of Agrochemistry and Food Technology (IATA-CSIC), 46980 Paterna, Spain; (A.S.); (M.C.C.)
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology (IATA-CSIC), 46980 Paterna, Spain; (A.S.); (M.C.C.)
| | - Marta Suárez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
| | - Laura Mantecón
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
| | - Gonzalo Solís
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
| | - Miguel Gueimonde
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.S.); (A.R.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
| | - Silvia Arboleya
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.S.); (A.R.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
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7
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Sanchez-Cid C, Ghaly TM, Gillings MR, Vogel TM. Sub-inhibitory gentamicin pollution induces gentamicin resistance gene integration in class 1 integrons in the environment. Sci Rep 2023; 13:8612. [PMID: 37244902 DOI: 10.1038/s41598-023-35074-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023] Open
Abstract
Antibiotics at sub-inhibitory concentrations are often found in the environment. Here they could impose selective pressure on bacteria, leading to the selection and dissemination of antibiotic resistance, despite being under the inhibitory threshold. The goal of this study was to evaluate the effects of sub-inhibitory concentrations of gentamicin on environmental class 1 integron cassettes in natural river microbial communities. Gentamicin at sub-inhibitory concentrations promoted the integration and selection of gentamicin resistance genes (GmRG) in class 1 integrons after only a one-day exposure. Therefore, sub-inhibitory concentrations of gentamicin induced integron rearrangements, increasing the mobilization potential of gentamicin resistance genes and potentially increasing their dissemination in the environment. This study demonstrates the effects of antibiotics at sub-inhibitory concentrations in the environment and supports concerns about antibiotics as emerging pollutants.
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Affiliation(s)
- Concepcion Sanchez-Cid
- Environmental Microbial Genomics, UMR 5005 Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, Écully, France.
| | - Timothy M Ghaly
- School of Natural Sciences, Macquarie University, NSW, 2109, Australia
| | - Michael R Gillings
- School of Natural Sciences, Macquarie University, NSW, 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, NSW, 2109, Australia
| | - Timothy M Vogel
- Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAe 1418, VetAgro Sup, Ecologie Microbienne, F-69622, Villeurbanne, France
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8
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Min J, Kim P, Yun S, Hong M, Park W. Zoo animal manure as an overlooked reservoir of antibiotic resistance genes and multidrug-resistant bacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:710-726. [PMID: 35906519 DOI: 10.1007/s11356-022-22279-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Animal fecal samples collected in the summer and winter from 11 herbivorous animals, including sable antelope (SA), long-tailed goral (LTG), and common eland (CE), at a public zoo were examined for the presence of antibiotic resistance genes (ARGs). Seven antibiotics, including meropenem and azithromycin, were used to isolate culturable multidrug-resistant (MDR) strains. The manures from three animals (SA, LTG, and CE) contained 104-fold higher culturable MDR bacteria, including Chryseobacterium, Sphingobacterium, and Stenotrophomonas species, while fewer MDR bacteria were isolated from manure from water buffalo, rhinoceros, and elephant against all tested antibiotics. Three MDR bacteria-rich samples along with composite samples were further analyzed using nanopore-based technology. ARGs including lnu(C), tet(Q), and mef(A) were common and often associated with transposons in all tested samples, suggesting that transposons carrying ARGs may play an important role for the dissemination of ARGs in our tested animals. Although several copies of ARGs such as aph(3')-IIc, blaL1, blaIND-3, and tet(42) were found in the sequenced genomes of the nine MDR bacteria, the numbers and types of ARGs appeared to be less than expected in zoo animal manure, suggesting that MDR bacteria in the gut of the tested animals had intrinsic resistant phenotypes in the absence of ARGs.
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Affiliation(s)
- Jihyeon Min
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Pureun Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Sohyeon Yun
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Minyoung Hong
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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9
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Yang MR, Wu YW. A Cross-Validated Feature Selection (CVFS) approach for extracting the most parsimonious feature sets and discovering potential antimicrobial resistance (AMR) biomarkers. Comput Struct Biotechnol J 2022; 21:769-779. [PMID: 36698972 PMCID: PMC9842539 DOI: 10.1016/j.csbj.2022.12.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022] Open
Abstract
Understanding genes and their underlying mechanisms is critical in deciphering how antimicrobial-resistant (AMR) bacteria withstand detrimental effects of antibiotic drugs. At the same time the genes related to AMR phenotypes may also serve as biomarkers for predicting whether a microbial strain is resistant to certain antibiotic drugs. We developed a Cross-Validated Feature Selection (CVFS) approach for robustly selecting the most parsimonious gene sets for predicting AMR activities from bacterial pan-genomes. The core idea behind the CVFS approach is interrogating features among non-overlapping sub-parts of the datasets to ensure the representativeness of the features. By randomly splitting the dataset into disjoint sub-parts, conducting feature selection within each sub-part, and intersecting the features shared by all sub-parts, the CVFS approach is able to achieve the goal of extracting the most representative features for yielding satisfactory AMR activity prediction accuracy. By testing this idea on bacterial pan-genome datasets, we showed that this approach was able to extract the most succinct feature sets that predicted AMR activities very well, indicating the potential of these genes as AMR biomarkers. The functional analysis demonstrated that the CVFS approach was able to extract both known AMR genes and novel ones, suggesting the capabilities of the algorithm in selecting relevant features and highlighting the potential of the novel genes in expanding the antimicrobial resistance gene databases.
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Affiliation(s)
- Ming-Ren Yang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, ROC,Department of Electrical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan, ROC
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, ROC,Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan, ROC,TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei 110, Taiwan, ROC,Correspondence to: Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250, Wuxing St., Sinyi Distr., Taipei 110, Taiwan, ROC.
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10
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Ramamurthy T, Ghosh A, Chowdhury G, Mukhopadhyay AK, Dutta S, Miyoshi SI. Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens. Front Cell Infect Microbiol 2022; 12:952491. [PMID: 36506027 PMCID: PMC9727169 DOI: 10.3389/fcimb.2022.952491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is an important global health problem affecting humans, animals, and the environment. AMR is considered as one of the major components in the "global one health". Misuse/overuse of antibiotics in any one of the segments can impact the integrity of the others. In the presence of antibiotic selective pressure, bacteria tend to develop several defense mechanisms, which include structural changes of the bacterial outer membrane, enzymatic processes, gene upregulation, mutations, adaptive resistance, and biofilm formation. Several components of mobile genetic elements (MGEs) play an important role in the dissemination of AMR. Each one of these components has a specific function that lasts long, irrespective of any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion sequence elements (ISs), and transposons carry the antimicrobial resistance genes (ARGs) on different genetic backbones. Successful transfer of ARGs depends on the class of plasmids, regulons, ISs proximity, and type of recombination systems. Additionally, phage-bacterial networks play a major role in the transmission of ARGs, especially in bacteria from the environment and foods of animal origin. Several other functional attributes of bacteria also get successfully modified to acquire ARGs. These include efflux pumps, toxin-antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling, quorum sensing, two-component system, and clustered regularly interspaced short palindromic repeats (CRISPR) systems. The metabolic and virulence state of bacteria is also associated with a range of genetic and phenotypic resistance mechanisms. In spite of the availability of a considerable information on AMR, the network associations between selection pressures and several of the components mentioned above are poorly understood. Understanding how a pathogen resists and regulates the ARGs in response to antimicrobials can help in controlling the development of resistance. Here, we provide an overview of the importance of genetic network and regulation of AMR in bacterial pathogens.
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Affiliation(s)
- Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India,*Correspondence: Thandavarayan Ramamurthy,
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K. Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-inchi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases at ICMR- National Institute of Cholera and Enteric Diseases, Kolkata, India,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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11
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Wang S, Wei L, Gao Y, Rong Y, Zha Z, Lv Y, Feng Z. Novel amikacin resistance genes identified from human gut microbiota by functional metagenomics. J Appl Microbiol 2022; 133:898-907. [PMID: 35543338 DOI: 10.1111/jam.15615] [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: 12/20/2021] [Revised: 03/10/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022]
Abstract
AIMS The aim of this study was to evaluate the diversity and potential for horizontal transfer of amikacin resistance genes from the human gut. METHODS AND RESULTS A library of human fecal microbiota was constructed and subjected to functional screening for amikacin resistance. In total, five amikacin resistance genes that conferred relatively high amikacin resistance, with minimum inhibitory concentrations (MICs) ranging from 64 to >512, were identified from the library, including a novel aminoglycoside acetyltransferase gene and a 16S rRNA methyltransferase (MTase) gene, labeled aac(6')-Iao and rmtI respectively. AAC(6')-Iao showed the highest identity of 48% to AAC(6')-Ian from a clinical isolate Serratia marcescens, whereas RmtI shared the closest amino acid identity of 32% with ArmA from Klebsiella pneumonia. The MICs of these five subclones to six commonly used aminoglycosides were determined. Susceptibility analysis indicated that RmtI was associated with high resistance phenotype to 4,6-disubstituted 2-DOS aminoglycosides, whereas AAC(6')-Iao conferred resistance to amikacin and kanamycin. In addition, kinetic parameters of AAC(6')-Iao were determined, suggesting a strong catalytic effect on amikacin and kanamycin. CONCLUSIONS Antibiotic resistance genes with low identity to known sequences can be uncovered by functional metagenomics. In addition, the diversity and prevalence of amikacin resistance genes merit further investigation in extended habitats, especially the 16S rRNA MTase gene that might have been underestimated in previous cognition. SIGNIFICANCE AND IMPACT OF STUDY Two novel amikacin resistance genes were identified in this study, including a 16S rRNA methyltransferase gene rmtI and an aminoglycoside acetyltransferase gene aac(6')-Iao. This work would contribute to the in-depth study of the diversity and horizontal transfer potential of amikacin resistance genes in the microbiome of the human gut.
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Affiliation(s)
- Shaochen Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Lin Wei
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuejiao Gao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yufeng Rong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhengqi Zha
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yunbin Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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12
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Gut microbiome in the emergence of antibiotic-resistant bacterial pathogens. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 192:1-31. [DOI: 10.1016/bs.pmbts.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Abstract
Antibiotic resistance is a global health challenge, involving the transfer of bacteria and genes between humans, animals and the environment. Although multiple barriers restrict the flow of both bacteria and genes, pathogens recurrently acquire new resistance factors from other species, thereby reducing our ability to prevent and treat bacterial infections. Evolutionary events that lead to the emergence of new resistance factors in pathogens are rare and challenging to predict, but may be associated with vast ramifications. Transmission events of already widespread resistant strains are, on the other hand, common, quantifiable and more predictable, but the consequences of each event are limited. Quantifying the pathways and identifying the drivers of and bottlenecks for environmental evolution and transmission of antibiotic resistance are key components to understand and manage the resistance crisis as a whole. In this Review, we present our current understanding of the roles of the environment, including antibiotic pollution, in resistance evolution, in transmission and as a mere reflection of the regional antibiotic resistance situation in the clinic. We provide a perspective on current evidence, describe risk scenarios, discuss methods for surveillance and the assessment of potential drivers, and finally identify some actions to mitigate risks.
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Affiliation(s)
- D. G. Joakim Larsson
- grid.8761.80000 0000 9919 9582Centre for Antibiotic Resistance Research at University of Gothenburg, Gothenburg, Sweden ,grid.8761.80000 0000 9919 9582Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- grid.8761.80000 0000 9919 9582Centre for Antibiotic Resistance Research at University of Gothenburg, Gothenburg, Sweden ,grid.8761.80000 0000 9919 9582Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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14
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A One-Health Genomic Investigation of Gentamicin Resistance in Salmonella from Human and Chicken Sources in Canada, 2014 to 2017. Antimicrob Agents Chemother 2021; 65:e0096621. [PMID: 34570642 DOI: 10.1128/aac.00966-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated whether the increased prevalence of gentamicin resistance in Salmonella from human infections was related to a similar increased prevalence in isolates from broiler chickens and whether this increase may have been due to coselection from use of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on gentamicin-resistant (Genr) Salmonella isolates from human and chicken sources collected from 2014 to 2017 by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). We determined the genomic relatedness of strains and characterized resistance genes and plasmids. From 2014 to 2017, 247 isolates of Genr Salmonella were identified by CIPARS: 188 were from humans, and 59 were from chicken sources (26 from live animals on farm and 33 from retail meat). The five most common Genr serovars were Salmonella enterica serovars Heidelberg (n = 93; 31.5%), 4,[5],12:i:- (n = 42; 14.2%), Kentucky (n = 37; 12.5%), Infantis (n = 33; 11.2%), and Typhimurium (n = 23; 7.8%). Phylogenomic analysis revealed that for S. Heidelberg and S. Infantis, there were closely related isolates from human and chicken sources. In both sources, resistance to gentamicin and spectinomycin was most frequently conferred by aac(3)-VIa and ant(3'')-Ia, respectively. Plasmid closure confirmed linkages of gentamicin and spectinomycin resistance genes and revealed instances of similar plasmids from both sources. Gentamicin and spectinomycin resistance genes were linked on the same plasmids, and some plasmids and isolates from humans and chickens were genetically similar, suggesting that the use of lincomycin-spectinomycin in chickens may be selecting for gentamicin-resistant Salmonella in broiler chickens and that these resistant strains may be acquired by humans.
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15
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Multicenter Clinical Evaluation Of ETEST® Plazomicin (PLZ) For Susceptibility Testing Of Enterobacterales. J Clin Microbiol 2021; 60:e0183121. [PMID: 34757833 PMCID: PMC8769719 DOI: 10.1128/jcm.01831-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plazomicin (PLZ), brand name ZEMDRI (Cipla Therapeutics), is a novel aminoglycoside antibiotic approved by the US Food and Drug Administration (FDA) for treatment of complicated urinary tract infections including pyelonephritis. ETEST® is a gradient diffusion method that represents an alternative to the more laborious broth micro-dilution (BMD) method for performing antimicrobial susceptibility testing (AST). A multi-center evaluation of the performance of the new ETEST® PLZ (bioMérieux) was conducted in comparison with BMD following FDA and International Standards Organization (ISO) recommendations using FDA-defined breakpoints. Clinical isolates of Enterobacterales (n=598) were included. Fifty-three isolates were resistant to PLZ according to BMD. Overall, the ETEST® PLZ demonstrated 99.0% Essential Agreement (EA), 92.8% Category Agreement (CA), 1.9% Very Major Errors (VME), 0% Major Errors (ME) and 7.0% minor Errors (mE) with both clinical and challenge isolates of Enterobacterales. The VME was found for a single Serratia marcescens strain. Individual species demonstrated EA rates ≥ 90%. In conclusion, we report that ETEST® PLZ represents an accurate tool for performing PLZ AST of Enterobacterales.
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16
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Ghaly TM, Gillings MR, Penesyan A, Qi Q, Rajabal V, Tetu SG. The Natural History of Integrons. Microorganisms 2021; 9:2212. [PMID: 34835338 PMCID: PMC8618304 DOI: 10.3390/microorganisms9112212] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 11/17/2022] Open
Abstract
Integrons were first identified because of their central role in assembling and disseminating antibiotic resistance genes in commensal and pathogenic bacteria. However, these clinically relevant integrons represent only a small proportion of integron diversity. Integrons are now known to be ancient genetic elements that are hotspots for genomic diversity, helping to generate adaptive phenotypes. This perspective examines the diversity, functions, and activities of integrons within both natural and clinical environments. We show how the fundamental properties of integrons exquisitely pre-adapted them to respond to the selection pressures imposed by the human use of antimicrobial compounds. We then follow the extraordinary increase in abundance of one class of integrons (class 1) that has resulted from its acquisition by multiple mobile genetic elements, and subsequent colonisation of diverse bacterial species, and a wide range of animal hosts. Consequently, this class of integrons has become a significant pollutant in its own right, to the extent that it can now be detected in most ecosystems. As human activities continue to drive environmental instability, integrons will likely continue to play key roles in bacterial adaptation in both natural and clinical settings. Understanding the ecological and evolutionary dynamics of integrons can help us predict and shape these outcomes that have direct relevance to human and ecosystem health.
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Affiliation(s)
- Timothy M. Ghaly
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
| | - Michael R. Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia;
| | - Anahit Penesyan
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia;
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Qin Qi
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
| | - Vaheesan Rajabal
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia;
| | - Sasha G. Tetu
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia;
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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17
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Allende A, Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson‐Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López‐Alonso M, Nielsen SS, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Innocenti ML, Liébana E, López‐Gálvez G, Manini P, Stella P, Peixe L. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed.
Part 2: Aminoglycosides/aminocyclitols: apramycin, paromomycin, neomycin and spectinomycin. EFSA J 2021; 19:e06853. [PMID: 34729082 PMCID: PMC8546520 DOI: 10.2903/j.efsa.2021.6853] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The specific concentrations of apramycin, paromomycin, neomycin and spectinomycin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield, were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC for these antimicrobials, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for apramycin and neomycin, whilst for paromomycin and spectinomycin, no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these four antimicrobials.
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18
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Liang J, Zhou K, Li Q, Dong X, Zhang P, Liu H, Lin H, Zhang X, Lu J, Lin X, Li K, Xu T, Zhang H, Bao Q, Zhu M, Hu Y, Ren P. Identification and Characterization of a Novel Aminoglycoside 3''-Nucleotidyltransferase, ANT(3'')-IId, From Acinetobacter lwoffii. Front Microbiol 2021; 12:728216. [PMID: 34531844 PMCID: PMC8438517 DOI: 10.3389/fmicb.2021.728216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/06/2021] [Indexed: 11/19/2022] Open
Abstract
A novel plasmid-encoded aminoglycoside 3''-nucleotidyltransferase ANT(3")-IId, was discovered in Acinetobacter lwoffi strain H7 isolated from a chick on an animal farm in Wenzhou, China. The whole-genome of A. lwoffii H7 consisted of one chromosome and five plasmids (pH7-250, pH7-108, pH7-68, pH7-48, and pH7-11). ant(3")-IId was identified as being encoded on pH7-250, sharing the highest amino acid identity of 50.64% with a function-known resistance gene, ant(3")-IIb (KB849358.1). Susceptibility testing and enzyme kinetic parameter analysis were conducted to determine the function of the aminoglycoside 3"-nucleotidyltransferase. The ant(3")-IId gene conferred resistance to spectinomycin and streptomycin [the minimum inhibitory concentration (MIC) levels of both increased 16-fold compared with the control strain]. Consistent with the MIC data, kinetic analysis revealed a narrow substrate profile including spectinomycin and streptomycin, with Kcat/Km ratios of 4.99 and 4.45×103M−1 S−1, respectively. Sequencing analysis revealed that the ant(3")-IId gene was associated with insertion sequences (IS) element [ΔISAba14-ΔISAba14-hp-orf-orf-orf1-ant(3")-IId], and ant(3")-IId were identified in plasmids from various Acinetobacter species. This study of the novel aminoglycoside 3"-nucleotidyltranferase ANT(3")-IId helps us further understand the functional and sequence characteristics of aminoglycoside 3"-nucleotidyltranferases, highlights the risk of resistance gene transfer among Acinetobacter species and suggests that attention should be given to the emergence of new aminoglycoside 3"-nucleotidyltranferase genes.
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Affiliation(s)
- Jialei Liang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kexin Zhou
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xu Dong
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Peiyao Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hongmao Liu
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hailong Lin
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Mei Zhu
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
| | - Yunliang Hu
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ping Ren
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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19
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Cama J, Leszczynski R, Tang PK, Khalid A, Lok V, Dowson CG, Ebata A. To Push or To Pull? In a Post-COVID World, Supporting and Incentivizing Antimicrobial Drug Development Must Become a Governmental Priority. ACS Infect Dis 2021; 7:2029-2042. [PMID: 33606496 PMCID: PMC7931625 DOI: 10.1021/acsinfecdis.0c00681] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The COVID-19 pandemic has refocused attention worldwide on the dangers of infectious diseases, in terms of both global health and the effects on the world economy. Even in high income countries, health systems have been found wanting in dealing with the new infectious agent. However, the even greater long-term danger of antimicrobial resistance in pathogenic bacteria and fungi is still under-appreciated, especially among the general public. Although antimicrobial drug development faces significant scientific challenges, the gravest challenge at the moment appears to be economic, where the lack of a viable market has led to a collapse in drug development pipelines. There is therefore a critical need for governments across the world to further incentivize the development of antimicrobials. Most incentive strategies over the past decade have focused on so-called "push" incentives that bridge the costs of antimicrobial research and development, but these have been insufficient for reviving the pipeline. In this Perspective, we analyze the current incentive strategies in place for antimicrobial drug development, and focus on "pull" incentives, which instead aim to improve revenue generation and thereby resolve the antimicrobial market failure challenge. We further analyze these incentives in a broader "One Health" context and stress the importance of developing and enforcing strict protocols to ensure appropriate manufacturing practices and responsible use. Our analysis reiterates the importance of international cooperation, coordination across antimicrobial research, and sustained funding in tackling this significant global challenge. A failure to invest wisely and continuously to incentivize antimicrobial pipelines will have catastrophic consequences for global health and wellbeing in the years to come.
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Affiliation(s)
- J. Cama
- Living
Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K.
- College
of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter EX4 4QF, U.K.
- ,
| | - R. Leszczynski
- Polygeia,
Global Health Student Think Tank, London, U.K.https://www.polygeia.com/
| | - P. K. Tang
- Polygeia,
Global Health Student Think Tank, London, U.K.https://www.polygeia.com/
- Faculty
of Life Sciences and Medicine, King’s
College London, Great
Maze Pond, London SE1 1UK, U.K.
| | - A. Khalid
- Polygeia,
Global Health Student Think Tank, London, U.K.https://www.polygeia.com/
- School
of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, U.K.
| | - V. Lok
- Polygeia,
Global Health Student Think Tank, London, U.K.https://www.polygeia.com/
- School of
Biological and Chemical Sciences, Queen
Mary University of London, Mile End Road, London E1 4NS, U.K.
| | - C. G. Dowson
- School
of Life Sciences, Gibbet Hill Campus, University
of Warwick, Coventry CV4 7AL, U.K.
- Antibiotic
Research U.K., Genesis 5, York Science Park, Heslington, York YO10 5DQ, U.K.
| | - A. Ebata
- Institute
of Development Studies, Library Road, Brighton BN1 9RE, U.K.
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20
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Lu W, Li K, Huang J, Sun Z, Li A, Liu H, Zhou D, Lin H, Zhang X, Li Q, Lu J, Lin X, Li P, Zhang H, Xu T, Bao Q. Identification and characteristics of a novel aminoglycoside phosphotransferase, APH(3')-IId, from an MDR clinical isolate of Brucella intermedia. J Antimicrob Chemother 2021; 76:2787-2794. [PMID: 34329431 DOI: 10.1093/jac/dkab272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To describe a novel chromosomal aminoglycoside phosphotransferase named APH(3')-IId identified in an MDR Brucella intermedia ZJ499 isolate from a cancer patient. METHODS Species identity was determined by PCR and MALDI-TOF MS analysis. WGS was performed to determine the genetic elements conferring antimicrobial resistance. Gene cloning, transcriptional analysis and targeted gene deletion, as well as protein purification and kinetic analysis, were performed to investigate the mechanism of resistance. RESULTS APH(3')-IId consists of 266 amino acids and shares the highest identity (48.25%) with the previously known APH(3')-IIb. Expression of aph(3')-IId in Escherichia coli decreased susceptibility to kanamycin, neomycin, paromomycin and ribostamycin. The aph(3')-IId gene in ZJ499 was transcriptionally active under laboratory conditions and the relative abundance of this transcript was unaffected by treatment with the above four antibiotics. However, deletion of aph(3')-IId in ZJ499 results in decreased MICs of these drugs. The purified APH(3')-IId showed phosphotransferase activity against kanamycin, neomycin, paromomycin and ribostamycin, with catalytic efficiencies (kcat/Km) ranging from ∼105 to 107 M-1 s-1. Genetic environment and comparative genomic analyses suggested that aph(3')-IId is probably a ubiquitous gene in Brucella, with no mobile genetic elements detected in its surrounding region. CONCLUSIONS APH(3')-IId is a novel chromosomal aminoglycoside phosphotransferase and plays an important role in the resistance of B. intermedia ZJ499 to kanamycin, neomycin, paromomycin and ribostamycin. To the best of our knowledge, APH(3')-IId represents the fourth characterized example of an APH(3')-II enzyme.
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Affiliation(s)
- Wei Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Jiansheng Huang
- The Fifth Affiliated Hospital, Wenzhou Medical University, Lishui, Zhejiang 323000, China
| | - Zhewei Sun
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Aifang Li
- The Fifth Affiliated Hospital, Wenzhou Medical University, Lishui, Zhejiang 323000, China
| | - Hongmao Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Danying Zhou
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Hailong Lin
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Xueya Zhang
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Qiaoling Li
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Peizhen Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Hailin Zhang
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Teng Xu
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Translational Medicine, Baotou Central Hospital, Baotou 014040, China
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
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21
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Hao H, Liu Y, Cao J, Gao K, Lu Y, Wang W, Wang P, Lu S, Hu L, Tong Z, Li W. Genomic New Insights Into Emergence and Clinical Therapy of Multidrug-Resistant Klebsiella pneumoniae in Infected Pancreatic Necrosis. Front Microbiol 2021; 12:669230. [PMID: 34248878 PMCID: PMC8269854 DOI: 10.3389/fmicb.2021.669230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Infected pancreatic necrosis (IPN) is a key risk factor in the progression of severe acute pancreatitis, and use of antibiotics is one of the main clinical actions. However, early prophylactic or unreasonable use of antibiotics promotes drug resistance in bacteria and also delays optimum treatment. To explore genomic evidence of rational antibiotic use in intensive care units, we isolated Klebsiella pneumoniae from IPN samples that showed the highest positive-culture rate in 758 patients. Based on whole-genome sequencing from eight strains, 42 antibiotic-resistant genes were identified in the chromatin and 27 in the plasmid, which included classic resistance-mechanism factors such as β-lactamases [16.67% (7/42) in the chromatin and 25.93% (7/27) in the plasmid]. The K. pneumoniae isolates were identified to be resistant to multiple antibiotics used in clinics. In vivo and in vitro, ceftazidime-avibactam (CZA) plus aztreonam (ATM) (2.5:1) showed more significant antibacterial effectiveness than CZA alone. The isolated K. pneumoniae were of three different types according to the resistance phenotypes for CZA and ATM. Those co-harboring bla NDM-5, bla CTX-M-15, bla OXA-1, and bla SHV-187 showed higher resistance to CAZ than bla NDM-5. Those co-harboring bla CTX-M-65, bla SHV-182, and bla TEM-181 were significantly less resistant to β-lactam than to other extended-spectrum β-lactamases. However, β-lactamases were inhibited by avibactam (AVI), except for NDM-5. ATM plus AVI showed a significant inhibitory effect on K. pneumoniae, and the minimum dosage of ATM was < 1 mg/L. In conclusion, we propose that ATM plus AVI could be a major therapy for complex infectious diseases caused by multidrug-resistant K. pneumoniae.
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Affiliation(s)
- Haibin Hao
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yang Liu
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jin Cao
- Laboratory of Microbiology, Basic Medical Laboratory, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Kun Gao
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.,School of Medicine, Nanjing Medical University, Nanjing, China
| | - Yingying Lu
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.,School of Medicine, Southeast University, Nanjing, China
| | - Weiping Wang
- Laboratory of Microbiology, Basic Medical Laboratory, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Peng Wang
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Sida Lu
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Long Hu
- Department of Bioinformatics, Hugobiotech Co., Ltd., Beijing, China
| | - Zhihui Tong
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Weiqin Li
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.,National Institut of Healthcare Data Science at Nanjing University, Nanjing, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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22
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Kim DW, Cha CJ. Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission. Exp Mol Med 2021; 53:301-309. [PMID: 33642573 PMCID: PMC8080597 DOI: 10.1038/s12276-021-00569-z] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 01/31/2023] Open
Abstract
The concept of the antibiotic resistome was introduced just over a decade ago, and since then, active resistome studies have been conducted. In the present study, we describe the previously established concept of the resistome, which encompasses all types of antibiotic resistance genes (ARGs), and the important findings from each One-Health sector considering this concept, thereby emphasizing the significance of the One-Health approach in understanding ARG transmission. Cutting-edge research methodologies are essential for deciphering the complex resistome structure in the microbiomes of humans, animals, and the environment. Based on the recent achievements of resistome studies in multiple One-Health sectors, future directions for resistome research have been suggested to improve the understanding and control of ARG transmission: (1) ranking the critical ARGs and their hosts; (2) understanding ARG transmission at the interfaces of One-Health sectors; (3) identifying selective pressures affecting the emergence, transmission, and evolution of ARGs; and (4) elucidating the mechanisms that allow an organism to overcome taxonomic barriers in ARG transmission.
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Affiliation(s)
- Dae-Wi Kim
- grid.411545.00000 0004 0470 4320Division of Life Sciences, Jeonbuk National University, Jeonju, 54896 Republic of Korea
| | - Chang-Jun Cha
- grid.254224.70000 0001 0789 9563Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546 Republic of Korea
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23
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Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data. J Microbiol 2021; 59:270-280. [DOI: 10.1007/s12275-021-0652-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 12/13/2022]
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24
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McGivern BB, McDonell RK, Morris SK, LaPara TM, Donato JJ. Novel class 1 integron harboring antibiotic resistance genes in wastewater-derived bacteria as revealed by functional metagenomics. Plasmid 2021; 114:102563. [PMID: 33515651 DOI: 10.1016/j.plasmid.2021.102563] [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: 10/21/2020] [Revised: 01/19/2021] [Accepted: 01/23/2021] [Indexed: 11/15/2022]
Abstract
Combatting antibiotic resistance is critical to our ability to treat infectious diseases. Here, we identified and characterized diverse antimicrobial resistance genes, including potentially mobile elements, from synthetic wastewater treatment microcosms exposed to the antibacterial agent triclosan. After seven weeks of exposure, the microcosms were subjected to functional metagenomic selection across 13 antimicrobials. This was achieved by cloning the combined genetic material from the microcosms, introducing this genetic library into E. coli, and selecting for clones that grew on media supplemented with one of the 13 antimicrobials. We recovered resistant clones capable of growth on media supplemented with a single antimicrobial, yielding 13 clones conferring resistance to at least one antimicrobial agent. Antibiotic susceptibility analysis revealed resistance ranging from 4 to >50 fold more resistant, while one clone showed resistance to multiple antibiotics. Using both Sanger and SMRT sequencing, we identified the predicted active gene(s) on each clone. One clone that conferred resistance to tetracycline contained a gene encoding a novel tetA-type efflux pump that was named TetA(62). Three clones contained predicted active genes on class 1 integrons. One integron had a previously unreported genetic arrangement and was named In1875. This study demonstrated the diversity and potential for spread of resistance genes present in human-impacted environments.
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Affiliation(s)
- Bridget B McGivern
- Chemistry Department, University of St. Thomas, St. Paul, MN 55105, United States of America
| | - Rylie K McDonell
- Chemistry Department, University of St. Thomas, St. Paul, MN 55105, United States of America
| | - Sydney K Morris
- Chemistry Department, University of St. Thomas, St. Paul, MN 55105, United States of America
| | - Timothy M LaPara
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, MN 55455, United States of America
| | - Justin J Donato
- Chemistry Department, University of St. Thomas, St. Paul, MN 55105, United States of America.
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25
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Osei Sekyere J, Reta MA. Global evolutionary epidemiology and resistome dynamics of Citrobacter species, Enterobacter hormaechei, Klebsiella variicola, and Proteeae clones. Environ Microbiol 2021; 23:7412-7431. [PMID: 33415808 DOI: 10.1111/1462-2920.15387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/03/2021] [Indexed: 12/15/2022]
Abstract
Citrobacter spp., Enterobacter hormaechei subsp., Klebsiella variicola and Proteae tribe members are rarely isolated Enterobacterales increasingly implicated in nosocomial infections. Herein, we show that these species contain multiple genes encoding resistance to important antibiotics and are widely and globally distributed, being isolated from human, animal, plant, and environmental sources in 67 countries. Certain clones and clades of these species were internationally disseminated, serving as reservoirs and mediums for the global dissemination of antibiotic resistance genes. As they can easily transmit these genes to more pathogenic species, additional molecular surveillance studies should be undertaken to identify and contain these antibiotic-resistant species.
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Affiliation(s)
- John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Prinshof, Pretoria, Gauteng, South Africa
| | - Melese Abate Reta
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Prinshof, Pretoria, Gauteng, South Africa
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26
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Milaković M, Križanović S, Petrić I, Šimatović A, González-Plaza JJ, Gužvinec M, Andrašević AT, Pole L, Fuka MM, Udiković-Kolić N. Characterization of macrolide resistance in bacteria isolated from macrolide-polluted and unpolluted river sediments and clinical sources in Croatia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:142357. [PMID: 33370905 DOI: 10.1016/j.scitotenv.2020.142357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/10/2020] [Accepted: 09/10/2020] [Indexed: 06/12/2023]
Abstract
Environments polluted with excessively high levels of antibiotics released from manufacturing sites can act as a source of transferable antibiotic resistance (AR) genes to human commensal and pathogenic bacteria. The aim of this study was to evaluate AR of bacteria isolated from the Sava river sediments (Croatia) at the discharge site of effluents from azithromycin production compared to those from the upstream site and isolates collected in Croatian hospitals. A total of 228 environmental strains of azithromycin-resistant bacteria were isolated and identified, with 124 from the discharge site and 104 from the upstream site. In addition, a total of 90 clinical, azithromycin-resistant streptococcal and staphylococcal isolates obtained from the Croatian Reference Center for Antibiotic Resistance Surveillance were analyzed. PCR screening of isolates on 11 relevant macrolide-resistance genes (MRGs) showed that discharge isolates had greater detection frequencies for 4 gene targets (ermB, msrE, mphE and ermF) compared to upstream isolates. Among clinical isolates, the most frequently detected gene was ermB, followed by msrD, mefE and mefC. The discharge site demonstrated a greater abundance of isolates with co-occurrence of two different MRGs (predominantly msrE-mphE) than the upstream site, but a lower abundance than the clinical sources (most commonly msrD-mefE). The simultaneous presence of three or even four MRGs was specific for the discharge and clinical isolates, but not for the upstream isolates. When MRG results were sorted by gene mechanism, the ribosomal methylation (erm) and protection genes (msr) were the most frequently detected among both the discharge and the clinical isolates. Following sequencing, high nucleotide sequence similarity was observed between ermB in the discharge isolates and the clinical streptococcal isolates, suggesting a possible transfer of the ermB gene between bacteria of clinical and environmental origin. Our study highlights the importance of environmental bacterial populations as reservoirs for clinically relevant macrolide-resistance genes.
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Affiliation(s)
- Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Stela Križanović
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ines Petrić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ana Šimatović
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Juan J González-Plaza
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Marija Gužvinec
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000 Zagreb, Croatia
| | - Arjana Tambić Andrašević
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000 Zagreb, Croatia
| | - Lucia Pole
- Department of Microbiology, University of Zagreb, Faculty of Agriculture, Svetošimunska 25, 10 000 Zagreb, Croatia
| | - Mirna Mrkonjić Fuka
- Department of Microbiology, University of Zagreb, Faculty of Agriculture, Svetošimunska 25, 10 000 Zagreb, Croatia
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia.
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27
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The Class A Carbapenemases BKC-1 and GPC-1 Both Originate from the Bacterial Genus Shinella. Antimicrob Agents Chemother 2020; 64:AAC.01263-20. [PMID: 32958716 PMCID: PMC7674036 DOI: 10.1128/aac.01263-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/16/2020] [Indexed: 02/06/2023] Open
Abstract
Comparative genomics identified the environmental bacterial genus Shinella as the most likely origin of the class A carbapenemases BKC-1 and GPC-1. Available sequences and PCR analyses of additional Shinella species revealed homologous β-lactamases showing up to 85.4% and 93.3% amino acid identity to both enzymes, respectively. The genes conferred resistance to β-lactams once expressed in Escherichia coli. blaBKC-1 likely evolved from a putative ancestral Shinella gene with higher homology through duplication of a gene fragment. Comparative genomics identified the environmental bacterial genus Shinella as the most likely origin of the class A carbapenemases BKC-1 and GPC-1. Available sequences and PCR analyses of additional Shinella species revealed homologous β-lactamases showing up to 85.4% and 93.3% amino acid identity to both enzymes, respectively. The genes conferred resistance to β-lactams once expressed in Escherichia coli. blaBKC-1 likely evolved from a putative ancestral Shinella gene with higher homology through duplication of a gene fragment.
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28
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Identification of a Novel Plasmid-Borne Gentamicin Resistance Gene in Nontyphoidal Salmonella Isolated from Retail Turkey. Antimicrob Agents Chemother 2020; 64:AAC.00867-20. [PMID: 32816720 DOI: 10.1128/aac.00867-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/06/2020] [Indexed: 12/19/2022] Open
Abstract
The spread of antibiotic-resistant bacteria presents a global health challenge. Efficient surveillance of bacteria harboring antibiotic resistance genes (ARGs) is a critical aspect to controlling the spread. Increased access to microbial genomic data from many diverse populations informs this surveillance but only when functional ARGs are identifiable within the data set. Current, homology-based approaches are effective at identifying the majority of ARGs within given clinical and nonclinical data sets for several pathogens, yet there are still some whose identities remain elusive. By coupling phenotypic profiling with genotypic data, these unknown ARGs can be identified to strengthen homology-based searches. To prove the efficacy and feasibility of this approach, a published data set from the U.S. National Antimicrobial Resistance Monitoring System (NARMS), for which the phenotypic and genotypic data of 640 Salmonella isolates are available, was subjected to this analysis. Six isolates recovered from the NARMS retail meat program between 2011 and 2013 were identified previously as phenotypically resistant to gentamicin but contained no known gentamicin resistance gene. Using the phenotypic and genotypic data, a comparative genomics approach was employed to identify the gene responsible for the observed resistance in all six of the isolates. This gene, grdA, is harbored on a 9,016-bp plasmid that is transferrable to Escherichia coli, confers gentamicin resistance to E. coli, and has never before been reported to confer gentamicin resistance. Bioinformatic analysis of the encoded protein suggests an ATP binding motif. This work demonstrates the advantages associated with coupling genomics technologies with phenotypic data for novel ARG identification.
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29
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Abstract
The emergence and spread of antibiotic resistance genes (ARGs) among pathogens threaten the prevention and treatment of bacterial infections as well as our food production chains. Early knowledge about mobile ARGs that are present in pathogens or that have the potential to become clinically relevant could help mitigate potential negative consequences. Recently, exploring integron gene cassettes was shown to be successful for identifying novel mobilized ARGs, some of which were already circulating in pathogens. Still, only a subset of ARGs is mobilized by integrons, and the contexts of other mobile genetic elements associated with ARGs remain unexplored. This includes insertion sequences (ISs) responsible for the mobilization of many ARGs. Our analyses identified ISs, species, and environments where ARG-IS relationships are particularly strong. This could be a first step to guide the discovery of novel ARGs, while also providing insights into mechanisms involved in the mobilization and transfer of ARGs. Insertion sequences (ISs) are abundant mobile genetic elements on bacterial genomes, responsible for mobilization of many genes, including antibiotic resistance genes (ARGs). As ARGs often occur in similar genetic contexts, understanding which ISs tend to be associated with known ARGs could be a first step toward discovering novel ARGs through predictive or experimental strategies. This could be valuable, as early identification of ARGs in pathogens could facilitate surveillance, confinement actions, molecular diagnostics, and drug development. Here, we present a comprehensive analysis of the association of specific ISs with known ARGs. A large collection of bacterial genomes was used to characterize the immediate context of 2,437 known ARGs and 3,768 ISs. While many ARGs were consistently found close to specific ISs, the contexts around all ISs were more variable. Nevertheless, a subset of individual ISs, as well as tentative composite transposons, showed significant associations with ARGs. These included, e.g., insertion sequences classified as IS6, Tn3, IS4, and IS1 that were not only strongly associated with diverse ARGs but also highly abundant in pathogens. Therefore, we conclude that the context of this subset of ISs and tentative composite transposons would be particularly valuable to discover novel ARGs through modeling or empirical approaches. A set of 1,891 metagenomes were analyzed to identify environments where those ISs commonly associated with ARGs were particularly abundant. The associations found in metagenomes were similar to those found in genomes. IMPORTANCE The emergence and spread of antibiotic resistance genes (ARGs) among pathogens threaten the prevention and treatment of bacterial infections as well as our food production chains. Early knowledge about mobile ARGs that are present in pathogens or that have the potential to become clinically relevant could help mitigate potential negative consequences. Recently, exploring integron gene cassettes was shown to be successful for identifying novel mobilized ARGs, some of which were already circulating in pathogens. Still, only a subset of ARGs is mobilized by integrons, and the contexts of other mobile genetic elements associated with ARGs remain unexplored. This includes insertion sequences (ISs) responsible for the mobilization of many ARGs. Our analyses identified ISs, species, and environments where ARG-IS relationships are particularly strong. This could be a first step to guide the discovery of novel ARGs, while also providing insights into mechanisms involved in the mobilization and transfer of ARGs.
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30
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Shewanella harboring antimicrobial and copper resistance genes in sea urchins (Paracentrotus lividus) from the Crozon peninsula (Brittany, France). INFECTION GENETICS AND EVOLUTION 2020; 85:104437. [PMID: 32574704 DOI: 10.1016/j.meegid.2020.104437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 12/21/2022]
Abstract
Shewanella is a genus of aquatic non-fermenting Gram-negative bacteria with increasing numbers of reports of infections in humans and appearance of antimicrobial resistant strains. Cases of infection show a relatively strong association with seafood consumption or exposure to seawater. This study aimed to analyze Shewanella spp. isolated from the sea urchin Paracentrotus lividus collected from the Crozon peninsula (France) with the intention of obtaining insights into the role of this genus as a reservoir of antimicrobial and heavy metal resistance genes. Five among seven Shewanella isolates were resistant to antimicrobials, mainly to broad spectrum beta-lactams. Four isolates displayed multiple resistance to at least three of these antimicrobial classes: broad spectrum beta-lactams, aminoglycosides, macrolide, quinolones and/or tetracycline. Three antimicrobial resistance genes were detected in just one isolate encoding resistance to beta-lactam (blaSHV and blaTEM-1) and macrolide (ermB). In addition, the copper resistance gene cusB, was observed in this isolate which is also a plasmid carrier. Another copper resistance encoding gene, copA, was found among the isolates. These results indicate that the multidrug-resistant (MDR) Shewanella isolates and resistance genes could be potential risks to public health, due to the carrying of these MDR bacteria by sea urchins through human consumption.
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31
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González Plaza JJ. Small RNAs as Fundamental Players in the Transference of Information During Bacterial Infectious Diseases. Front Mol Biosci 2020; 7:101. [PMID: 32613006 PMCID: PMC7308464 DOI: 10.3389/fmolb.2020.00101] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/04/2020] [Indexed: 12/24/2022] Open
Abstract
Communication shapes life on Earth. Transference of information has played a paramount role on the evolution of all living or extinct organisms since the appearance of life. Success or failure in this process will determine the prevalence or disappearance of a certain set of genes, the basis of Darwinian paradigm. Among different molecules used for transmission or reception of information, RNA plays a key role. For instance, the early precursors of life were information molecules based in primitive RNA forms. A growing field of research has focused on the contribution of small non-coding RNA forms due to its role on infectious diseases. These are short RNA species that carry out regulatory tasks in cis or trans. Small RNAs have shown their relevance in fine tuning the expression and activity of important regulators of essential genes for bacteria. Regulation of targets occurs through a plethora of mechanisms, including mRNA stabilization/destabilization, driving target mRNAs to degradation, or direct binding to regulatory proteins. Different studies have been conducted during the interplay of pathogenic bacteria with several hosts, including humans, animals, or plants. The sRNAs help the invader to quickly adapt to the change in environmental conditions when it enters in the host, or passes to a free state. The adaptation is achieved by direct targeting of the pathogen genes, or subversion of the host immune system. Pathogens trigger also an immune response in the host, which has been shown as well to be regulated by a wide range of sRNAs. This review focuses on the most recent host-pathogen interaction studies during bacterial infectious diseases, providing the perspective of the pathogen.
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Affiliation(s)
- Juan José González Plaza
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
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Kwiecień E, Stefańska I, Chrobak-Chmiel D, Sałamaszyńska-Guz A, Rzewuska M. New Determinants of Aminoglycoside Resistance and Their Association with the Class 1 Integron Gene Cassettes in Trueperella pyogenes. Int J Mol Sci 2020; 21:E4230. [PMID: 32545831 PMCID: PMC7352783 DOI: 10.3390/ijms21124230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 12/15/2022] Open
Abstract
Trueperella pyogenes is an important opportunistic animal pathogen. Different antimicrobials, including aminoglycosides, are used to treat T. pyogenes infections. The aim of the present study was to evaluate aminoglycoside susceptibility and to detect aminoglycoside resistance determinants in 86 T. pyogenes isolates of different origin. Minimum inhibitory concentration of gentamicin, streptomycin, and kanamycin was determined using a standard broth microdilution method. Genetic elements associated with aminoglycoside resistance were investigated by PCR and DNA sequencing. All studied isolates were susceptible to gentamicin, but 32.6% and 11.6% of them were classified as resistant to streptomycin and kanamycin, respectively. A total of 30 (34.9%) isolates contained class 1 integrons. Class 1 integron gene cassettes carrying aminoglycoside resistance genes, aadA11 and aadA9, were found in seven and two isolates, respectively. Additionally, the aadA9 gene found in six isolates was not associated with mobile genetic elements. Moreover, other, not carried by gene cassettes, aminoglycoside resistance genes, strA-strB and aph(3')-IIIa, were also detected. Most importantly, this is the first description of all reported genes in T. pyogenes. Nevertheless, the relevance of the resistance phenotype to genotype was not perfectly matched in 14 isolates. Therefore, further investigations are needed to fully explain aminoglycoside resistance mechanisms in T. pyogenes.
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Affiliation(s)
| | | | | | | | - Magdalena Rzewuska
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8 St., 02-786 Warsaw, Poland; (E.K.); (I.S.); (D.C.-C.); (A.S.-G.)
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Böhm ME, Razavi M, Flach CF, Larsson DGJ. A Novel, Integron-Regulated, Class C β-Lactamase. Antibiotics (Basel) 2020; 9:antibiotics9030123. [PMID: 32183280 PMCID: PMC7148499 DOI: 10.3390/antibiotics9030123] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/26/2022] Open
Abstract
AmpC-type β-lactamases severely impair treatment of many bacterial infections, due to their broad spectrum (they hydrolyze virtually all β-lactams, except fourth-generation cephalosporins and carbapenems) and the increasing incidence of plasmid-mediated versions. The original chromosomal AmpCs are often tightly regulated, and their expression is induced in response to exposure to β-lactams. Regulation of mobile ampC expression is in many cases less controlled, giving rise to constitutively resistant strains with increased potential for development or acquisition of additional resistances. We present here the identification of two integron-encoded ampC genes, blaIDC-1 and blaIDC-2 (integron-derived cephalosporinase), with less than 85% amino acid sequence identity to any previously annotated AmpC. While their resistance pattern identifies them as class C β-lactamases, their low isoelectric point (pI) values make differentiation from other β-lactamases by isoelectric focusing impossible. To the best of our knowledge, this is the first evidence of an ampC gene cassette within a class 1 integron, providing a mobile context with profound potential for transfer and spread into clinics. It also allows bacteria to adapt expression levels, and thus reduce fitness costs, e.g., by cassette-reshuffling. Analyses of public metagenomes, including sewage metagenomes, show that the discovered ampCs are primarily found in Asian countries.
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Affiliation(s)
- Maria-Elisabeth Böhm
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; (M.-E.B.); (M.R.); (C.-F.F.)
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Mohammad Razavi
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; (M.-E.B.); (M.R.); (C.-F.F.)
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; (M.-E.B.); (M.R.); (C.-F.F.)
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - D. G. Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; (M.-E.B.); (M.R.); (C.-F.F.)
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
- Correspondence:
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