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Hou Z, Xu B, Liu L, Yan R, Zhang J. Isolation, Identification, Antimicrobial Resistance, Genotyping, and Whole-Genome Sequencing Analysis of Salmonella Enteritidis Isolated from a Food-Poisoning Incident. Pol J Microbiol 2024; 73:69-89. [PMID: 38437471 PMCID: PMC10911658 DOI: 10.33073/pjm-2024-008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 01/21/2024] [Indexed: 03/06/2024] Open
Abstract
Salmonella enterica is a common pathogen in humans and animals that causes food poisoning and infection, threatening public health safety. We aimed to investigate the genome structure, drug resistance, virulence characteristics, and genetic relationship of a Salmonella strain isolated from patients with food poisoning. The pathogen strain 21A was collected from the feces of patients with food poisoning, and its minimum inhibitory concentration against commonly used antibiotics was determined using the strip test and Kirby-Bauer disk methods. Subsequently, WGS analysis was used to reveal the genome structural characteristics and the carrying status of resistance genes and virulence genes of strain 21A. In addition, an MLST-based minimum spanning tree and an SNP-based systematic spanning tree were constructed to investigate its genetic evolutionary characteristics. The strain 21A was identified by mass spectrometry as S. enterica, which was found to show resistance to ampicillin, piperacillin, sulbactam, levofloxacin, and ciprofloxacin. The WGS and bioinformatics analyses revealed this strain as Salmonella Enteritidis belonging to ST11, which is common in China, containing various resistance genes and significant virulence characteristics. Strain 21A was closely related to the SJTUF strains, a series strains from animal, food and clinical sources, as well as from Shanghai, China, which were located in the same evolutionary clade. According to the genetic makeup of strain 21A, the change G > A was found to be the most common variation. We have comprehensively analyzed the genomic characteristics, drug resistance phenotype, virulence phenotype, and genetic evolution relationship of S. Enteritidis strain 21A, which will contribute towards an in-depth understanding of the pathogenic mechanism of S. Enteritidis and the effective prevention and control of foodborne diseases.
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Affiliation(s)
- Zhuru Hou
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
- Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, China
| | - Benjin Xu
- Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, China
- Department of Medical Laboratory Science, Fenyang College of Shanxi Medical University, Fenyang, China
- Department of Clinical Laboratory, Fenyang Hospital of Shanxi Province, Fenyang, China
| | - Ling Liu
- Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, China
- Department of Medical Laboratory Science, Fenyang College of Shanxi Medical University, Fenyang, China
- Department of Clinical Laboratory, Fenyang Hospital of Shanxi Province, Fenyang, China
| | - Rongrong Yan
- Department of Clinical Laboratory, Fenyang Hospital of Shanxi Province, Fenyang, China
| | - Jinjing Zhang
- Department of Clinical Laboratory, Fenyang Hospital of Shanxi Province, Fenyang, China
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Hernández Flores JL, Martínez YJ, Ramos López MÁ, Saldaña Gutierrez C, Reyes AA, Armendariz Rosales MM, Cortés Pérez MJ, Mendoza MF, Ramírez Ramírez J, Zavala GR, Tovar Becerra PL, Valdez Santoyo L, Villasana Rodríguez K, Rodríguez Morales JA, Campos Guillén J. Volatile Organic Compounds Produced by Kosakonia cowanii Cp1 Isolated from the Seeds of Capsicum pubescens R & P Possess Antifungal Activity. Microorganisms 2023; 11:2491. [PMID: 37894149 PMCID: PMC10609226 DOI: 10.3390/microorganisms11102491] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 10/01/2023] [Indexed: 10/29/2023] Open
Abstract
The Kosakonia cowanii Cp1 strain was isolated from seeds of Capsicum pubescens R. & P. cultivated in Michoacan, Mexico. Genetic and ecological role analyses were conducted for better characterization. The results show that genome has a length of 4.7 Mbp with 56.22% G + C and an IncF plasmid of 128 Kbp with 52.51% G + C. Furthermore, pathogenicity test revealed nonpathogenic traits confirmed by the absence of specific virulence-related genes. Interestingly, when fungal inhibitory essays were carried out, the bacterial synthesis of volatile organic compounds (VOCs) with antifungal activity showed that Sclerotinia sp. and Rhizoctonia solani were inhibited by 87.45% and 77.24%, respectively. Meanwhile, Sclerotium rolfsii, Alternaria alternata, and Colletotrichum gloeosporioides demonstrated a mean radial growth inhibition of 52.79%, 40.82%, and 55.40%, respectively. The lowest inhibition was by Fusarium oxysporum, with 10.64%. The VOCs' characterization by headspace solid-phase microextraction combined with gas chromatography-mass spectrometry (HS-SPME-GC-MS) revealed 65 potential compounds. Some of the compounds identified with high relative abundance were ketones (22.47%), represented by 2-butanone, 3-hydroxy (13.52%), and alcohols (23.5%), represented by ethanol (5.56%) and 1-butanol-3-methyl (4.83%). Our findings revealed, for the first time, that K. cowanii Cp1 associated with C. pubescens seeds possesses potential traits indicating that it could serve as an effective biocontrol.
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Affiliation(s)
| | - Yomaiko Javier Martínez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Miguel Ángel Ramos López
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Carlos Saldaña Gutierrez
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Querétaro 76220, Mexico;
| | - Aldo Amaro Reyes
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Mariem Monserrat Armendariz Rosales
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Maraly Jazmin Cortés Pérez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Mayela Fosado Mendoza
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Joanna Ramírez Ramírez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Grecia Ramírez Zavala
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Paola Lizeth Tovar Becerra
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Laila Valdez Santoyo
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Karen Villasana Rodríguez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | | | - Juan Campos Guillén
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
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Hadchity L, Houard J, Lanois A, Payelleville A, Nassar F, Gualtieri M, Givaudan A, Abi Khattar Z. The AcrAB efflux pump confers self-resistance to stilbenes in Photorhabdus laumondii. Res Microbiol 2023; 174:104081. [PMID: 37196776 DOI: 10.1016/j.resmic.2023.104081] [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: 03/03/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
The Resistance-nodulation-division (RND)-type AcrAB-TolC efflux pump contributes to multidrug resistance in Gram-negative bacteria. Recently, the bacterium Photorhabdus laumondii TT01 has emerged as a goldmine for novel anti-infective drug discovery. Outside plants, Photorhabdus is the only Gram-negative known to produce stilbene-derivatives including 3,5-dihydroxy-4-ethyl-trans-stilbene and 3,5-dihydroxy-4-isopropyl-trans-stilbene (IPS). IPS is a bioactive polyketide which received considerable attention, mainly because of its antimicrobial properties, and is currently in late-stage clinical development as a topical treatment for psoriasis and dermatitis. To date, little is known about how Photorhabdus survives in the presence of stilbenes. We combined genetic and biochemical approaches to assess whether AcrAB efflux pump exports stilbenes in P. laumondii. We demonstrated that the wild-type (WT) exerts an antagonistic activity against its derivative ΔacrA mutant, and that is able to outcompete it in a dual-strain co-culture assay. The ΔacrA mutant also showed high sensitivity to 3,5-dihydroxy-4-ethyl-trans-stilbene and IPS as well as decreased IPS concentrations in its supernatant comparing to the WT. We report here a mechanism of self-resistance against stilbene derivatives of P. laumondii TT01, which enables these bacteria to survive under high concentrations of stilbenes by extruding them out via the AcrAB efflux pump.
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Affiliation(s)
- Linda Hadchity
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology Team, Faculty of Sciences 2, Lebanese University, P.O.Box 90656, Jdeidet El-Metn, Lebanon; DGIMI, Université Montpellier, INRAE, Montpellier, France.
| | | | - Anne Lanois
- DGIMI, Université Montpellier, INRAE, Montpellier, France.
| | - Amaury Payelleville
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium.
| | - Fida Nassar
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology Team, Faculty of Sciences 2, Lebanese University, P.O.Box 90656, Jdeidet El-Metn, Lebanon.
| | | | - Alain Givaudan
- DGIMI, Université Montpellier, INRAE, Montpellier, France.
| | - Ziad Abi Khattar
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology Team, Faculty of Sciences 2, Lebanese University, P.O.Box 90656, Jdeidet El-Metn, Lebanon.
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Hadchity L, Lanois A, Kiwan P, Nassar F, Givaudan A, Khattar ZA. AcrAB, the major RND-type efflux pump of Photorhabdus laumondii, confers intrinsic multidrug-resistance and contributes to virulence in insects. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:637-648. [PMID: 34002534 DOI: 10.1111/1758-2229.12974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
The resistance-nodulation-division (RND)-type efflux pumps AcrAB and MdtABC contribute to multidrug-resistance (MDR) in Gram-negative bacteria. Photorhabdus is a symbiotic bacterium of soil nematodes that also produces virulence factors killing insects by septicaemia. We previously showed that mdtA deletion in Photorhabdus laumondii TT01 resulted in no detrimental phenotypes. Here, we investigated the roles of the last two putative RND transporters in TT01 genome, AcrAB and AcrAB-like (Plu0759-Plu0758). Only ΔacrA and ΔmdtAΔacrA mutants were multidrug sensitive, even to triphenyltetrazolium chloride and bromothymol blue used for Photorhabdus isolation from nematodes on the nutrient bromothymol blue-triphenyltetrazolium chloride agar (NBTA) medium. Both mutants also displayed slightly attenuated virulence after injection into Spodoptera littoralis. Transcriptional analysis revealed intermediate levels of acrAB expression in vitro, in vivo and post-mortem, whereas its putative transcriptional repressor acrR was weakly expressed. Yet, plasmid-mediated acrR overexpression did not decrease acrAB transcript levels neither MDR in TT01 WT. While no pertinent mutations were detected in acrR of the same P. laumondii strain grown either on NBTA or nutrient agar, we suggest that AcrR-mediated repression of acrAB is not physiologically required under conditions tested. Finally, we propose that AcrAB is the primary RND-efflux pump, which is essential for MDR in Photorhabdus and may confer adaptive advantages during insect infection.
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Affiliation(s)
- Linda Hadchity
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology team, Faculty of Sciences 2, Lebanese University, Fanar, Lebanon
- DGIMI, Université Montpellier, INRAE, Montpellier, France
| | - Anne Lanois
- DGIMI, Université Montpellier, INRAE, Montpellier, France
| | - Paloma Kiwan
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology team, Faculty of Sciences 2, Lebanese University, Fanar, Lebanon
| | - Fida Nassar
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology team, Faculty of Sciences 2, Lebanese University, Fanar, Lebanon
| | - Alain Givaudan
- DGIMI, Université Montpellier, INRAE, Montpellier, France
| | - Ziad Abi Khattar
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology team, Faculty of Sciences 2, Lebanese University, Fanar, Lebanon
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Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics. Appl Environ Microbiol 2021; 87:AEM.02684-20. [PMID: 33547058 PMCID: PMC8091117 DOI: 10.1128/aem.02684-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study aimed to detect the cecal microbiome, antimicrobial resistance (AMR) and heavy metal resistance genes (MRGs) in fattening pigs raised under antibiotic-free (ABF) conditions compared with ordinary industrial pigs (control, C) using whole-genome shotgun sequencing. ABF pigs showed the enrichment of Prevotella (33%) and Lactobacillus (13%), whereas Escherichia coli (40%), Fusobacterium and Bacteroides (each at 4%) were notably observed in the C group. Distinct clusters of cecal microbiota of ABF and C pigs were revealed; however, microbiota of some C pigs (C1) appeared in the same cluster as ABF and were totally separated from the remaining C pigs (C2). For AMR genes, the highest abundance tet(Q) (35.7%) and mef(A) (12.7%) were markedly observed in the ABF group whereas tet(Q) (26.2%) and tet(W) (10.4%) were shown in the C group. tet(Q) was positively correlated to Prevotella in ABF and C1 samples. In the C2 group, the prominent tet(W) was positively correlated to Fusobacterium and Bacteroides Pigs have never received tetracycline but pregnant sows used chlortetracycline once 7 d before parturition. Chromosomal Cu and Zn resistance genes were also shown in both groups regardless the received Cu and Zn feed additives. A higher abundance of multi-metal resistance genes was observed in the C group (44%) compared with the ABF group (41%). In conclusion, the microbiome clusters in some C pigs were similar to that in ABF pigs. High abundant tetracycline resistance genes interrelated to major bacteria were observed in both ABF and C pigs. MRGs were also observed.IMPORTANCE: Owing to the increased problem of AMR in farm animals, raising farm animals without antibiotics is one method that could solve this problem. Our study showed that only some tetracycline and macrolide resistance genes, tet(Q), tet(W) and mef(A), were markedly abundant in ABF and C groups. The tet(Q) and tet(W) genes interrelated to different predominant bacteria in each group, showing the potential role of major bacteria as reservoirs of AMR genes. In addition, chromosomal Cu and Zn resistance genes were also observed in both pig groups, not depending on the use of Cu and Zn additives in both farms. The association of MRGs and AMR genotypes and phenotypes together with the method to re-sensitize bacteria to antibiotics should be studied further to unveil the cause of high resistance genes and solve the problems.
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Górecki K, McEvoy MM. Phylogenetic analysis reveals an ancient gene duplication as the origin of the MdtABC efflux pump. PLoS One 2020; 15:e0228877. [PMID: 32050009 PMCID: PMC7015380 DOI: 10.1371/journal.pone.0228877] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/23/2020] [Indexed: 11/19/2022] Open
Abstract
The efflux pumps from the Resistance-Nodulation-Division family, RND, are main contributors to intrinsic antibiotic resistance in Gram-negative bacteria. Among this family, the MdtABC pump is unusual by having two inner membrane components. The two components, MdtB and MdtC are homologs, therefore it is evident that the two components arose by gene duplication. In this paper, we describe the results obtained from a phylogenetic analysis of the MdtBC pumps in the context of other RNDs. We show that the individual inner membrane components (MdtB and MdtC) are conserved throughout the Proteobacterial species and that their existence is a result of a single gene duplication. We argue that this gene duplication was an ancient event which occurred before the split of Proteobacteria into Alpha-, Beta- and Gamma- classes. Moreover, we find that the MdtABC pumps and the MexMN pump from Pseudomonas aeruginosa share a close common ancestor, suggesting the MexMN pump arose by another gene duplication event of the original Mdt ancestor. Taken together, these results shed light on the evolution of the RND efflux pumps and demonstrate the ancient origin of the Mdt pumps and suggest that the core bacterial efflux pump repertoires have been generally stable throughout the course of evolution.
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Affiliation(s)
- Kamil Górecki
- Institute for Society & Genetics, University of California, Los Angeles, California, United States of America
| | - Megan M. McEvoy
- Institute for Society & Genetics, University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
- * E-mail:
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