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Kim MB, Lee YJ. Emergence of Salmonella Infantis carrying the pESI-like plasmid from eggs in egg grading and packing plants in Korea. Food Microbiol 2024; 122:104568. [PMID: 38839227 DOI: 10.1016/j.fm.2024.104568] [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: 03/04/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024]
Abstract
The plasmid of emerging S. Infantis (pESI) or pESI-like plasmid in Salmonella enterica Infantis are consistently reported in poultry and humans worldwide. However, there has been limited research on these plasmids of S. Infantis isolated from eggs. Therefore, this study aimed to analyze the prevalence and characteristics of S. Infantis carrying the pESI-like plasmid from eggs in egg grading and packing plants. In this study, the pESI-like plasmid was only detected in 18 (78.3%) of 23 S. Infantis isolates, and it was absent in the other 9 Salmonella serovars. In particular, S. Infantis isolates carrying the pESI-like plasmid showed the significantly higher resistance to β-lactams, phenicols, cephams, aminoglycosides, quinolones, sulfonamides, and tetracyclines than Salmonella isolates without the pESI-like plasmid (p < 0.05). Moreover, all S. Infantis isolates carrying the pESI-like plasmid were identified as extended-spectrum β-lactamase (ESBL) producer, harboring the blaCTX-M-65 and blaTEM-1 genes, and carried non-β-lactamase resistance genes (ant(3'')-Ia, aph(4)-Ia, aac(3)-IVa, aph(3')-Ic, sul1, tetA, dfrA14, and floR) against five antimicrobial classes. However, all isolates without the pESI-like plasmid only carried the blaTEM-1 gene among the β-lactamase genes, and either had no non-β-lactamase resistance genes or harbored non-β-lactamase resistance genes against one or two antimicrobial classes. Furthermore, all S. Infantis isolates carrying the pESI-like plasmid carried class 1 and 2 integrons and the aadA1 gene cassette, but none of the other isolates without the pESI-like plasmid harbored integrons. In particular, D87Y substitution in the gyrA gene and IncP replicon type were observed in all the S. Infantis isolates carrying the pESI-like plasmid but not in the S. Infantis isolates without the pESI-like plasmid. The distribution of pulsotypes between pESI-positive and pESI-negative S. Infantis isolates was clearly distinguished, but all S. Infantis isolates were classified as sequence type 32, regardless of whether they carried the pESI-like plasmid. This study is the first to report the characteristics of S. Infantis carrying the pESI-like plasmid isolated from eggs and can provide valuable information for formulating strategies to control the spread of Salmonella in the egg industry worldwide.
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Affiliation(s)
- Min Beom Kim
- College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu, 41556, Republic of Korea.
| | - Young Ju Lee
- College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu, 41556, Republic of Korea.
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Boff L, de Sousa Duarte H, Kraychete GB, Taddeucci-Rocha G, Oliveira BD, Albano RM, D'Alincourt Carvalho-Assef AP, Superti SV, Martins IS, Picão RC. Comparative analysis of the antimicrobial resistance and virulence traits in ESBL-producing-Klebsiella pneumoniae ST307 strains colonizing the gastrointestinal tract and causing a fatal bloodstream infection in a leukemia patient. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 121:105598. [PMID: 38653335 DOI: 10.1016/j.meegid.2024.105598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Klebsiella pneumoniae is an opportunistic pathogen that can colonize the gastrointestinal tract (GIT) of humans. The mechanisms underlying the successful translocation of this pathogen to cause extra-intestinal infections remain unknown, although virulence and antimicrobial resistance traits likely play significant roles in the establishment of infections. We investigated K. pneumoniae strains isolated from GIT colonization (strains Kp_FZcol-1, Kp_FZcol-2 and Kp_FZcro-1) and from a fatal bloodstream infection (strain Kp_HM-1) in a leukemia patient. All strains belonged to ST307, carried a transferable IncF plasmid containing the blaCTX-M-15 gene (pKPN3-307 TypeA-like plasmid) and showed a multidrug-resistance phenotype. Phylogenetic analysis demonstrated that Kp_HM-1 was more closely related to Kp_FZcro-1 than to the other colonizing strains. The Kp_FZcol-2 genome showed 81 % coverage with the Kp_HM-1 246,730 bp plasmid (pKp_HM-1), lacking most of its putative virulence genes. Searching public genomes with similar coverage, we observed the occurrence of this deletion in K. pneumoniae ST307 strains recovered from human colonization and infection in different countries. Our findings suggest that strains lacking the putative virulence genes found in the pKPN3-307 TypeA plasmid are still able to colonize and infect humans, highlighting the need to further investigate the role of these genes for the adaptation of K. pneumoniae ST307 in distinct human body sites.
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Affiliation(s)
- Luana Boff
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Humberlânia de Sousa Duarte
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriela Bergiante Kraychete
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel Taddeucci-Rocha
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bianca Diniz Oliveira
- Hospital do Câncer I, Instituto Nacional do Câncer (INCA), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodolpho Mattos Albano
- Departamento de Bioquímica, Instituto de Biologia Roberto de Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Silvana Vargas Superti
- Hospital do Câncer I, Instituto Nacional do Câncer (INCA), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ianick Souto Martins
- Hospital do Câncer I, Instituto Nacional do Câncer (INCA), Rio de Janeiro, Rio de Janeiro, Brazil; Escola de Medicina, Universidade Federal Fluminense, Niterói, Brazil
| | - Renata Cristina Picão
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Departamento de Hidrobiologia, Universidade Federal de São Carlos, São Carlos, Brazil.
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Zhang Z, Kuang D, Xu X, Zhan Z, Ren H, Shi C. Dissemination of IncC plasmids in Salmonella enterica serovar Thompson recovered from seafood and human diarrheic patients in China. Int J Food Microbiol 2024; 417:110708. [PMID: 38653121 DOI: 10.1016/j.ijfoodmicro.2024.110708] [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: 12/18/2023] [Revised: 03/26/2024] [Accepted: 04/13/2024] [Indexed: 04/25/2024]
Abstract
Salmonella Thompson is a prevalent foodborne pathogen and a major threat to food safety and public health. This study aims to reveal the dissemination mechanism of S. Thompson with co-resistance to ceftriaxone and ciprofloxacin. In this study, 181 S. Thompson isolates were obtained from a retrospective screening on 2118 serotyped Salmonella isolates from foods and patients, which were disseminated in 12 of 16 districts in Shanghai, China. A total of 10 (5.5 %) S. Thompson isolates exhibited resistance to ceftriaxone (MIC ranging from 8 to 32 μg/mL) and ciprofloxacin (MIC ranging from 2 to 8 μg/mL). The AmpC β-lactamase gene blaCMY-2 and plasmid-mediated quinolone resistance (PMQR) genes of qnrS and qepA were identified in the 9 isolates. Conjugation results showed that the co-transfer of blaCMY-2, qnrS, and qepA occurred on the IncC plasmids with sizes of ∼150 (n = 8) or ∼138 (n = 1) kbp. Three typical modules of ISEcp1-blaCMY-2-blc-sugE, IS26-IS15DIV-qnrS-ISKpn19, and ISCR3-qepA-intl1 were identified in an ST3 IncC plasmid pSH11G0791. Phylogenetic analysis indicated that IncC plasmids evolved into Lineages 1, 2, and 3. IncC plasmids from China including pSH11G0791 in this study fell into Lineage 1 with those from the USA, suggesting their close genotype relationship. In conclusion, to our knowledge, it is the first report of the co-existence of blaCMY-2, qnrS, and qepA in IncC plasmids, and the conjugational transfer contributed to their dissemination in S. Thompson. These findings underline further challenges for the prevention and treatment of Enterobacteriaceae infections posed by IncC plasmids bearing blaCMY-2, qnrS, and qepA.
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Affiliation(s)
- Zengfeng Zhang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dai Kuang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China; National Health Commission (NHC) Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, China
| | - Xuebin Xu
- Laboratory of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200050, China
| | - Zeqiang Zhan
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Ren
- Xianyang Center for Food and Drug Control, Shaanxi, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.
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Puangseree J, Prathan R, Srisanga S, Chuanchuen R. Molecular basis of the persistence of chloramphenicol resistance among Escherichia coli and Salmonella spp. from pigs, pork and humans in Thailand. PLoS One 2024; 19:e0304250. [PMID: 38787814 PMCID: PMC11125496 DOI: 10.1371/journal.pone.0304250] [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: 03/03/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
This study aimed to investigate the potential mechanisms associated with the persistence of chloramphenicol (CHP) resistance in Escherichia coli and Salmonella enterica isolated from pigs, pork, and humans in Thailand. The CHP-resistant E. coli (n = 106) and Salmonella (n = 57) isolates were tested for their CHP susceptibility in the presence and absence of phenylalanine arginine β-naphthylamide (PAβN). The potential co-selection of CHP resistance was investigated through conjugation experiments. Whole genome sequencing (WGS) was performed to analyze the E. coli (E329, E333, and E290) and Salmonella (SA448, SA461, and SA515) isolates with high CHP MIC (32-256 μg/mL) and predominant plasmid replicon types. The presence of PAβN significantly reduced the CHP MICs (≥4-fold) in most E. coli (67.9%) and Salmonella (64.9%). Ampicillin, tetracycline, and streptomycin co-selected for CHP-resistant Salmonella and E. coli-transconjugants carrying cmlA. IncF plasmids were mostly detected in cmlA carrying Salmonella (IncFIIAs) and E. coli (IncFIB and IncF) transconjugants. The WGS analysis revealed that class1 integrons with cmlA1 gene cassette flanked by IS26 and TnAs1 were located on IncX1 plasmid, IncFIA(HI1)/HI1B plasmids and IncFII/FIB plasmids. IncFIA(HI1)/HI1B/Q1in SA448 contained catA flanked by IS1B and TnAs3. In conclusion, cross resistance through proton motive force-dependent mechanisms and co-selection by other antimicrobial agents involved the persistence of CHP-resistance in E. coli in this collection. Dissemination of CHP-resistance genes was potentially facilitated by mobilization via mobile genetic elements.
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Affiliation(s)
- Jiratchaya Puangseree
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Rangsiya Prathan
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Center for Antimicrobial Resistance Monitoring in Food-borne Pathogens, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Songsak Srisanga
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Center for Antimicrobial Resistance Monitoring in Food-borne Pathogens, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Rungtip Chuanchuen
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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Garrido V, Arrieta-Gisasola A, Migura-García L, Laorden L, Grilló MJ. Multidrug resistance in Salmonella isolates of swine origin: mobile genetic elements and plasmids associated with cephalosporin resistance with potential transmission to humans. Appl Environ Microbiol 2024; 90:e0026424. [PMID: 38695519 PMCID: PMC11107176 DOI: 10.1128/aem.00264-24] [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: 02/13/2024] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
The emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context requiring continuous surveillance. Resistance to ciprofloxacin and cephalosporins is of particular concern. Since pigs are a relevant source of foodborne Salmonella for human beings, we studied transmissible AMR genes and MGE in a collection of 83 strains showing 9 different serovars and 15 patterns of multidrug resistant (MDR) previously isolated from pigs raised in the conventional breeding system of Northern Spain. All isolates were susceptible to ciprofloxacin and three isolates carried blaCMY-2 or blaCTX-M-9 genes responsible for cefotaxime resistance. Filter mating experiments showed that the two plasmids carrying blaCTX-M-9 were conjugative while that carrying blaCMY-2 was self-transmissible by transformation. Whole-genome sequencing and comparative analyses were performed on the isolates and plasmids. The IncC plasmid pSB109, carrying blaCMY-2, was similar to one found in S. Reading from cattle, indicating potential horizontal transfer between serovars and animal sources. The IncHI2 plasmids pSH102 in S. Heidelberg and pSTM45 in S. Typhimurium ST34, carrying blaCTX-M-9, shared similar backbones and two novel "complex class 1 integrons" containing different AMR and heavy metal genes. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.IMPORTANCEThe emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context. Since pigs are a relevant source of foodborne Salmonella for humans, in this study, we investigate different aspects of AMR in a collection of 83 Salmonella showing nine different serovars and 15 patterns of multidrug resistant (MDR) isolated from pigs raised in the conventional breeding system. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.
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Affiliation(s)
- V. Garrido
- Instituto de Agrobiotecnología (IdAB; CSIC-Gobierno de Navarra), Mutilva, Navarra, Spain
| | - A. Arrieta-Gisasola
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, MikroIker Research Group, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - L. Migura-García
- Joint Research Unit IRTA-UAB in Animal Health, Animal Health Research Centre (CReSA), Autonomous University of Barcelona (UAB), Catalonia, Spain
- Institute of Agrifood Research and Technology (IRTA), Animal Health Program (CReSA), WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
| | - L. Laorden
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, MikroIker Research Group, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - M. J. Grilló
- Instituto de Agrobiotecnología (IdAB; CSIC-Gobierno de Navarra), Mutilva, Navarra, Spain
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Bandić Pavlović D, Pospišil M, Nađ M, Vrbanović Mijatović V, Luxner J, Zarfel G, Grisold A, Tonković D, Dobrić M, Bedenić B. Multidrug-Resistant Bacteria in Surgical Intensive Care Units: Antibiotic Susceptibility and β-Lactamase Characterization. Pathogens 2024; 13:411. [PMID: 38787264 PMCID: PMC11124292 DOI: 10.3390/pathogens13050411] [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: 04/07/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Multidrug-resistant (MDR) bacteria of the utmost importance are extended-spectrum β-lactamase (ESBL) and carbapenemase-producing Enterobacterales (CRE), carbapenem-resistant Acinetobacter baumannii (CRAB), carbapenem-resistant Pseudomonas aeruginosa (CRPA), methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus spp. (VRE). In this study, an evaluation of MDR bacteria in surgical intensive care units in a tertiary referral hospital was conducted. The study aimed to characterize β-lactamases and other resistance traits of Gram-negative bacteria isolated in surgical intensive care units (ICUs). Disk diffusion and the broth dilution method were used for antibiotic susceptibility testing, whereas ESBL screening was performed through a double disk synergy test and an inhibitor-based test with clavulanic acid. A total of 119 MDR bacterial isolates were analysed. ESBL production was observed in half of the Proteus mirabilis, 90% of the Klebsiella pneumoniae and all of the Enterobacter cloacae and Escherichia coli isolates. OXA-48 carbapenemase, carried by the L plasmid, was detected in 34 K. pneumoniae and one E. coli and Enterobacter cloacae complex isolates, whereas NDM occurred sporadically and was identified in three K. pneumoniae isolates. OXA-48 positive isolates coharboured ESBLs belonging to the CTX-M family in all but one isolate. OXA-23 carbapenemase was confirmed in all A. baumannii isolates. The findings of this study provide valuable insight of resistance determinants of Enterobacterales and A. baumannii which will enhance surveillance and intervention strategies that are necessary to curb the ever-growing carbapenem resistance rates.
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Affiliation(s)
- Daniela Bandić Pavlović
- Department of Anesthesiology and Intensive Care, University of Zagreb School of Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia; (D.B.P.); (V.V.M.); (D.T.)
| | - Mladen Pospišil
- Department of Emergency Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia;
| | - Marina Nađ
- University of Zagreb School of Medicine, 10000 Zagreb, Croatia;
| | - Vilena Vrbanović Mijatović
- Department of Anesthesiology and Intensive Care, University of Zagreb School of Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia; (D.B.P.); (V.V.M.); (D.T.)
| | - Josefa Luxner
- Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria; (J.L.); (G.Z.); (A.G.)
| | - Gernot Zarfel
- Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria; (J.L.); (G.Z.); (A.G.)
| | - Andrea Grisold
- Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria; (J.L.); (G.Z.); (A.G.)
| | - Dinko Tonković
- Department of Anesthesiology and Intensive Care, University of Zagreb School of Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia; (D.B.P.); (V.V.M.); (D.T.)
| | - Mirela Dobrić
- Department of Anesthesiology, Intensive Medicine and Pain Management, University Hospital Centre Sestre Milosrdnice, 10000 Zagreb, Croatia;
| | - Branka Bedenić
- Biomedical Research Center Šalata—BIMIS, Department for Clinical Microbiology and Infection Prevention and Control, University of Zagreb School of Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
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Bocanegra-Ibarias P, Duran-Bedolla J, Silva-Sánchez J, Garza-Ramos U, Sánchez-Pérez A, Garza-Gonzáles E, Morfín-Otero R, Barrios-Camacho H. Identification of Providencia spp. clinical isolates co-producing carbapenemases IMP-27, OXA-24, and OXA-58 in Mexico. Diagn Microbiol Infect Dis 2024; 109:116246. [PMID: 38452556 DOI: 10.1016/j.diagmicrobio.2024.116246] [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: 10/12/2023] [Revised: 01/20/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Providencia rettgeri, belonging to the genus Providencia, had gained significant interest due to its increasing prevalence as a common pathogen responsible for healthcare-associated infections in hospitals. P. rettgeri isolates producing carbapenemases have been reported to reduce the efficiency of carbapenems in clinical antimicrobial therapy. However, coexistence with other resistance determinants is rarely reported. The goal of this study was the molecular characterization of carbapenemase-producing Providencia spp. clinical isolates. Among 23 Providencia spp. resistant to imipenem, 21 were positive to blaNDM-1; one positive to blaNDM-1 and blaOXA-58 like; and one isolate co-producing blaIMP-27, blaOXA-24/40 like, and blaOXA-58 like were identified. We observed a low clonal relationship, and the incompatibility groups Col3M and ColRNAI were identified in the plasmid harboring blaNDM-1. We report for the first time a P. rettgeri strain co-producing blaIMP-27, blaOXA-24-like, and blaOXA-58 like. The analysis of these resistance mechanisms in carbapenemase co-producing clinical isolates reflects the increased resistance.
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Affiliation(s)
- Paola Bocanegra-Ibarias
- Facultad de Medicina/Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología, Universidad Autónoma de Nuevo León, Monterrey, México
| | - Josefina Duran-Bedolla
- Departamento de Diagnóstico Epidemiológico, Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán. C.P. 62100, Morelos, Cuernavaca, México
| | - Jesús Silva-Sánchez
- Departamento de Diagnóstico Epidemiológico, Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán. C.P. 62100, Morelos, Cuernavaca, México
| | - Ulises Garza-Ramos
- Departamento de Diagnóstico Epidemiológico, Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán. C.P. 62100, Morelos, Cuernavaca, México
| | - Alejandro Sánchez-Pérez
- Departamento de Diagnóstico Epidemiológico, Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán. C.P. 62100, Morelos, Cuernavaca, México
| | - Elvira Garza-Gonzáles
- Facultad de Medicina/Hospital Universitario "Dr. José Eleuterio González", Laboratorio de Microbiología Molecular, Departamento de Bioquímica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, México
| | - Rayo Morfín-Otero
- Universidad de Guadalajara, Centro Universitario de Ciencias de la Salud, Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Guadalajara, México
| | - Humberto Barrios-Camacho
- Departamento de Diagnóstico Epidemiológico, Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán. C.P. 62100, Morelos, Cuernavaca, México.
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Moussa J, Nassour E, Jisr T, El Chaar M, Tokajian S. Characterization of blaNDM-19-producing IncX3 plasmid isolated from carbapenem-resistant Escherichia coli and Klebsiellapneumoniae. Heliyon 2024; 10:e29642. [PMID: 38655329 PMCID: PMC11036045 DOI: 10.1016/j.heliyon.2024.e29642] [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: 06/29/2023] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024] Open
Abstract
The increase in the prevalence of carbapenem-producing Enterobacterales (CPE) is a major threat, with the New Delhi metallo-β-lactamase (NDM) enzyme-producing CPEs being one of the major causative agents of healthcare settings infections. In this study, we characterized an IncX3 plasmid harboring blaNDM-19 in Lebanon, recovered from three Escherichia coli belonging to ST167 and one Klebsiella pneumoniae belonging to ST16 isolated from a clinical setting. Plasmid analysis using PBRT, Plasmid Finder, and PlasmidSPAdes showed that all four isolates carried a conjugative 47-kb plasmid having blaNDM-19, and was designated as pLAU-NDM19. We constructed a sequence-based maximum likelihood phylogenetic tree and compared pLAU-NDM19 to other representative IncX3 plasmids carrying NDM-variants and showed that it was closely linked to NDM-19 positive IncX3 plasmid from K. pneumoniae reported in China. Our findings also revealed the route mediating resistance transmission, the IncX3 dissemination among Enterobacterales, and the NDM-19 genetic environment. We showed that mobile elements contributed to the variability of IncX3 genomic environment and highlighted that clonal dissemination in healthcare settings facilitated the spread of resistance determinants. Antimicrobial stewardship programs implemented in hospitals should be coupled with genomic surveillance to better understand the mechanisms mediating the mobilization of resistance determinants among nosocomial pathogens and their subsequent clonal dissemination.
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Affiliation(s)
- Jennifer Moussa
- Department of Natural Sciences, Lebanese American University, P.O. Box 36, Byblos, Lebanon
| | - Elie Nassour
- Department of Natural Sciences, Lebanese American University, P.O. Box 36, Byblos, Lebanon
| | - Tamima Jisr
- Clinical Laboratory Department, Makassed General Hospital, P.O.Box 11-6301, Beirut, Lebanon
| | - Mira El Chaar
- Faculty of Health Sciences, University of Balamand, P.O. Box 55251, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, P.O. Box 36, Byblos, Lebanon
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Algarni S, Gudeta DD, Han J, Nayak R, Foley SL. Genotypic analyses of IncHI2 plasmids from enteric bacteria. Sci Rep 2024; 14:9802. [PMID: 38684834 PMCID: PMC11058233 DOI: 10.1038/s41598-024-59870-2] [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: 11/22/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Incompatibility (Inc) HI2 plasmids are large (typically > 200 kb), transmissible plasmids that encode antimicrobial resistance (AMR), heavy metal resistance (HMR) and disinfectants/biocide resistance (DBR). To better understand the distribution and diversity of resistance-encoding genes among IncHI2 plasmids, computational approaches were used to evaluate resistance and transfer-associated genes among the plasmids. Complete IncHI2 plasmid (N = 667) sequences were extracted from GenBank and analyzed using AMRFinderPlus, IntegronFinder and Plasmid Transfer Factor database. The most common IncHI2-carrying genera included Enterobacter (N = 209), Escherichia (N = 208), and Salmonella (N = 204). Resistance genes distribution was diverse, with plasmids from Escherichia and Salmonella showing general similarity in comparison to Enterobacter and other taxa, which grouped together. Plasmids from Enterobacter and other taxa had a higher prevalence of multiple mercury resistance genes and arsenic resistance gene, arsC, compared to Escherichia and Salmonella. For sulfonamide resistance, sul1 was more common among Enterobacter and other taxa, compared to sul2 and sul3 for Escherichia and Salmonella. Similar gene diversity trends were also observed for tetracyclines, quinolones, β-lactams, and colistin. Over 99% of plasmids carried at least 25 IncHI2-associated conjugal transfer genes. These findings highlight the diversity and dissemination potential for resistance across different enteric bacteria and value of computational-based approaches for the resistance-gene assessment.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Dereje D Gudeta
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Jing Han
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Rajesh Nayak
- Office of Regulatory Compliance and Risk Management, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Steven L Foley
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA.
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10
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Nery Garcia BL, Dantas STA, da Silva Barbosa K, Mendes Mitsunaga T, Butters A, Camargo CH, Nobrega DB. Extended-Spectrum Beta-Lactamase-Producing Escherichia coli and Other Antimicrobial-Resistant Gram-Negative Pathogens Isolated from Bovine Mastitis: A One Health Perspective. Antibiotics (Basel) 2024; 13:391. [PMID: 38786120 PMCID: PMC11117280 DOI: 10.3390/antibiotics13050391] [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: 03/31/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
Antimicrobial resistance (AMR) poses an imminent threat to global public health, driven in part by the widespread use of antimicrobials in both humans and animals. Within the dairy cattle industry, Gram-negative coliforms such as Escherichia coli and Klebsiella pneumoniae stand out as major causative agents of clinical mastitis. These same bacterial species are frequently associated with severe infections in humans, including bloodstream and urinary tract infections, and contribute significantly to the alarming surge in antimicrobial-resistant bacterial infections worldwide. Additionally, mastitis-causing coliforms often carry AMR genes akin to those found in hospital-acquired strains, notably the extended-spectrum beta-lactamase genes. This raises concerns regarding the potential transmission of resistant bacteria and AMR from mastitis cases in dairy cattle to humans. In this narrative review, we explore the distinctive characteristics of antimicrobial-resistant E. coli and Klebsiella spp. strains implicated in clinical mastitis and human infections. We focus on the molecular mechanisms underlying AMR in these bacterial populations and critically evaluate the potential for interspecies transmission. Despite some degree of similarity observed in sequence types and mobile genetic elements between strains found in humans and cows, the existing literature does not provide conclusive evidence to assert that coliforms responsible for mastitis in cows pose a direct threat to human health. Finally, we also scrutinize the existing literature, identifying gaps and limitations, and propose avenues for future research to address these pressing challenges comprehensively.
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Affiliation(s)
- Breno Luis Nery Garcia
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (B.L.N.G.); (S.T.A.D.); (K.d.S.B.); (T.M.M.)
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Stéfani Thais Alves Dantas
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (B.L.N.G.); (S.T.A.D.); (K.d.S.B.); (T.M.M.)
| | - Kristian da Silva Barbosa
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (B.L.N.G.); (S.T.A.D.); (K.d.S.B.); (T.M.M.)
| | - Thatiane Mendes Mitsunaga
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (B.L.N.G.); (S.T.A.D.); (K.d.S.B.); (T.M.M.)
| | - Alyssa Butters
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | | | - Diego Borin Nobrega
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
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11
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Banerjee J, Batabyal S, Biswas S, Bhattacharyya D, Habib M, Das AK, Nanda PK, Samanta I, Dandapat P, Bandyopadhyay S. Stray Dogs (Mongrels) Are Potent Reservoir of Drug-Resistant Pathogens: A Study in Peri-Urban Areas of Kolkata, India. Microb Drug Resist 2024. [PMID: 38656133 DOI: 10.1089/mdr.2023.0249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
This study depicts the drug-resistance and phylogenomic characteristics of 365 Escherichia coli (EC) and 76 Klebsiella pneumoniae (KP) isolated from stray dogs (293) in and around Kolkata, India. Initial screening found 59 isolates, including 48 E. coli and 11 KP multidrug resistant, which included 33 extended-spectrum β-lactamase, 41 AmpC β-lactamase and 18 metallo-β-lactamase producers carrying blaNDM-1 (11) and blaNDM-5 (7) genes. Majority of them had the resistant genes such as blaCTX-M (33), blaTEM (18), blaSHV (4), blaOXA (17), blaFOX (2), blaDHA (2), blaCITM (15), blaCMY-2 (13), blaGES (2) and blaVEB (2), qnrS (15), qnrB (3), aac-6'-Ib-cr (14), tetA (26), tetB (14), sul-1 (25), armA (2) and rmtB (6), in addition to adherence genes such as csgA (33), fimA (27), fliC (13), sdiA (33), rcsA (38), and rpoS (39). They also carried plasmid of diverse replicon types of which IncFIA and FIB were the most frequent. Phylogrouping categorized most of the MDR E. coli in phylogroup A (20), B1 (14), and B2 (6). Enterobacteriaceae repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) showed genetic diversity of multidrug resistant isolates irrespective of their origin, resistance, and virulence types, differentiating the EC in five clades (A-E) and KP in four clades (A-D). As these stray dogs, which had no history or scope of previous antimicrobial therapy, were found to have contracted potential antimicrobial resistance pathogens, the role of environment in spread of such pathogens and further possibility of human infections cannot be ruled out.
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Affiliation(s)
- Jaydeep Banerjee
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | - Subhasis Batabyal
- West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Suman Biswas
- West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | | | - Md Habib
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | - Arun K Das
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | - Pramod K Nanda
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | - Indranil Samanta
- West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Premanshu Dandapat
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
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12
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Qin J, Wang Z, Xu H, Li Y, Zhou J, Yaxier N, Wang C, Fu P. IncX3 plasmid-mediated spread of blaNDM gene in Enterobacteriaceae among children in China. J Glob Antimicrob Resist 2024; 37:199-207. [PMID: 38641225 DOI: 10.1016/j.jgar.2024.03.021] [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: 11/02/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/21/2024] Open
Abstract
OBJECTIVES The blaNDM gene was prevalent among children and became the predominant cause of severe infection in infants and children. This study aimed to investigate the epidemiology and molecular characteristics of blaNDM in Enterobacteriaceae among children in China. METHODS Carbapenem-resistant Enterobacteriaceae (CRE) were collected in the Children's Hospital of Fudan University from January 2016 to December 2022. Five carbapenemase genes (blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-48) were screened by PCR method. Multilocus sequence typing (MLST) was conducted for phylogenetic analyses. blaNDM-carrying plasmids were typed by PCR-based Incompatibility (Inc) typing method. Moreover, plasmid comparison was performed with 213 publicly available IncX3 plasmids. RESULTS A total of 330 CRE strains were enrolled, 96.4% of which carried carbapenemase genes. blaNDM gene accounted for 64.8% (214 strains) and included four variants, including blaNDM-1 (59.8%), blaNDM-5 (39.3%), blaNDM-7 (0.5%), and blaNDM-9 (0.5%). There were no predominant MLST lineages of blaNDM carrying strains. IncX3 was the major plasmid carrying blaNDM-1 (68.0%) and blaNDM-5 (72.6%) and was dominant in blaNDM-Klebsiella penumoniae (79.8%), blaNDM-Escherichia coli (58.2%), and blaNDM-Enterobacter cloacae (61.0%), respectively. Most (79.0%) clinical IncX3 plasmids in the world carried blaNDM, and the prevalence of blaNDM in IncX3 plasmids was more common in China (95.8%) than other countries (58.1%, P <0.01). CONCLUSION blaNDM is highly prevalent in CRE among children in China. The spread of blaNDM was mainly mediated by IncX3 plasmids. Surveillance and infection control on the spread of blaNDM among children are important.
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Affiliation(s)
- Jie Qin
- Lab of Microbiology, Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China
| | - Zixuan Wang
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China
| | - Huihui Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China
| | - Yijia Li
- Lab of Microbiology, Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China
| | - Jinlan Zhou
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China
| | - Nijiati Yaxier
- Orthopedics Department, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China
| | - Chuanqing Wang
- Lab of Microbiology, Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China; Nosocomial Infection Control Department, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China.
| | - Pan Fu
- Lab of Microbiology, Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China; Nosocomial Infection Control Department, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China.
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13
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Crippen TL, Sullivan JP, Anderson RC. Bacterial proximity effects on the transfer of antibiotic resistance genes within the alimentary tract of yellow mealworm larvae. JOURNAL OF ECONOMIC ENTOMOLOGY 2024; 117:417-426. [PMID: 38412361 DOI: 10.1093/jee/toae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/04/2024] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
The arthropod intestinal tract and other anatomical parts naturally carry microorganisms. Some of which are pathogens, secrete toxins, or carry transferable antibiotic-resistance genes. The risks associated with the production and consumption of edible arthropods are dependent on indigenous microbes, as well as microbes introduced during the processes of rearing. This mass arthropod production puts individual arthropods in close proximity, which increases the possibility of their exposure to antibiotic-resistant bacteria carried by bacteria from fellow insects, industry workers, or rearing hardware and substrates. The purpose of this study was to determine if the alimentary tract of the yellow mealworm provided an environment permitting horizontal gene transfer between bacteria. The effect of the concentration of bacterial exposure was also assessed. Antibiotic resistance gene transfer between marker Salmonella Lignières (Enterobacterales: Enterobacteriaceae) and Escherichia coli (Migula) (Enterobacterales: Enterobacteriaceae) introduced into the larval gut demonstrated that the nutrient-rich environment of the yellow mealworm gut provided favorable conditions for the transfer of antibiotic resistance genes. Conjugation frequencies were similar across inoculum concentrations; however, transconjugant production correlated positively to increased exposure concentration. The lowest concentration of bacterial exposure required enrichment to detect and thus may have been approaching a threshold level for the 2 bacteria to colocate within the expanse of the larval gut. While many factors can affect this transfer, the simple factor of the proximity of donor and recipient bacteria, as defined by the concentration of bacteria within the volume of the insect gut, likely primarily contributed to the efficiency of antibiotic gene transfer.
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Affiliation(s)
- Tawni L Crippen
- Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, 2881 F and B Road, College Station, TX 77845, USA
| | - John P Sullivan
- Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, 2881 F and B Road, College Station, TX 77845, USA
| | - Robin C Anderson
- Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, 2881 F and B Road, College Station, TX 77845, USA
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14
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Halder G, Chaudhury BN, Mandal S, Denny P, Sarkar D, Chakraborty M, Khan UR, Sarkar S, Biswas B, Chakraborty A, Maiti S, Dutta S. Whole genome sequence-based molecular characterization of blood isolates of carbapenem-resistant Enterobacter cloacae complex from ICU patients in Kolkata, India, during 2017-2022: emergence of phylogenetically heterogeneous Enterobacter hormaechei subsp. xiangfangensis. Microbiol Spectr 2024; 12:e0352923. [PMID: 38385742 PMCID: PMC10986559 DOI: 10.1128/spectrum.03529-23] [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: 09/29/2023] [Accepted: 12/14/2023] [Indexed: 02/23/2024] Open
Abstract
Blood-borne infections caused by the carbapenem-resistant Enterobacter cloacae complex (CR-ECC) are major public threats with respect to the challenges encountered during treatment. This study describes the whole genome sequencing-based molecular characteristics of blood isolates (n = 70) of CR-ECC from patients admitted to the intensive care unit of tertiary care hospitals in Kolkata, India, during 2017-2022 with respect to species identification, antimicrobial resistance (AMR) profiling, mechanism of drug resistance, and molecular subtypes. Vitek2 MALDI and species-specific PCR identified Enterobacter hormaechei subsp. xiangfangensis (47.14%) as the emerging CR-ECC subspecies in Kolkata. The predominating carbapenemase and extended-spectrum β-lactamase genes found were blaNDM-1 (51.42%) and blaCTX-M-15 (27%), respectively. Besides, blaNDM-4, blaNDM-5, blaNDM-7, blaCMH-3, blaSFO-1, blaOXA-181, blaOXA-232, blaKPC-3, and blaDHA-7 genes were also detected, which were not previously reported from India. A multitude of Class 1 integrons (including In180, In4874, In4887, and In4888, which were novel) and plasmid replicon types (IncFIB, IncFII, IncX3, IncHI1-HI2, IncC, and IncR) involved in AMR dissemination were identified. Reverse transcription-PCR and western blot revealed that carbapenem resistance in non-carbapenemase-producing CR-ECC isolates was contributed by elevated levels of ampC, overexpression of acrAB, and loss of ompF. A total of 30 distinct sequence types (STs) were ascertained by multi-locus sequence typing; of which, ST2011, ST2018, ST2055, ST2721, and ST2722 were novel STs. Pulsed-field gel electrophoresis analysis showed heterogeneity (69 pulsotypes with a similarity coefficient of 48.40%) among the circulating isolates, suggesting multiple reservoirs of infections in humans. Phylogenetically and genetically diverse CR-ECC with multiple AMR mechanisms mandates close monitoring of nosocomial infections caused by these isolates to forestall the transmission and dissemination of AMR.IMPORTANCEThe emergence and extensive dissemination of the carbapenem-resistant Enterobacter cloacae complex (CR-ECC) have positioned it as a critical nosocomial global pathogen. The dearth of a comprehensive molecular study pertaining to CR-ECC necessitated this study, which is the first of its kind from India. Characterization of blood isolates of CR-ECC over the last 6 years revealed Enterobacter hormaechei subsp. xiangfangensis as the most prevalent subsp., exhibiting resistance to almost all antibiotics currently in use and harboring diverse transmissible carbapenemase genes. Besides the predominating blaNDM-1 and blaCTX-M-15, we document diverse carbapenemase and AmpC genes, such as blaNDM-4, blaNDM-7, blaOXA-181, blaOXA-232, blaKPC-3, blaCMH-3, blaSFO-1, and blaDHA-7, in CR-ECC, which were not previously reported from India. Furthermore, novel integrons and sequence types were identified. Our findings emphasize the need for strengthened vigilance for molecular epidemiological surveillance of CR-ECC due to the presence of epidemic clones with a phylogenetically diverse and wide array of antimicrobial resistance genes in vulnerable populations.
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Affiliation(s)
- Gourab Halder
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | | | | | - Priyanka Denny
- Collaborative Research Center for Infectious Diseases in India, Okayama University, JICA Building, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Deotima Sarkar
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Mandira Chakraborty
- Division of Microbiology, Calcutta Medical College, College Square, Kolkata, India
| | - Ujjwayini Ray Khan
- Division of Microbiology, Apollo Gleneagles Hospital, Phool Bagan, Kolkata, India
| | - Soma Sarkar
- Division of Microbiology, NRS Medical College, Sealdah, Kolkata, India
| | | | | | - Sourav Maiti
- Division of Microbiology, Ruby General Hospital, Kasba, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
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15
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Chen Y, Liu L, Guo Y, Chu J, Wang B, Sui Y, Wei H, Hao H, Huang L, Cheng G. Distribution and genetic characterization of fluoroquinolone resistance gene qnr among Salmonella strains from chicken in China. Microbiol Spectr 2024; 12:e0300023. [PMID: 38411972 PMCID: PMC10986518 DOI: 10.1128/spectrum.03000-23] [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: 08/02/2023] [Accepted: 11/06/2023] [Indexed: 02/28/2024] Open
Abstract
The prevalence and dissemination of the plasmid-mediated fluoroquinolone (FQ) resistance gene qnr in Salmonella are considered serious public health concerns worldwide. So far, no comprehensive large-scale studies have focused on the prevalence and genetic characteristics of the qnr gene in Salmonella isolated from chickens. Herein, this study aimed to investigate the prevalence, antimicrobial resistance (AMR) patterns, and molecular characteristics of chicken-originated qnr-positive Salmonella strains from chicken farms, slaughterhouses, and markets in 12 provinces of China in 2020-2021. The overall prevalence of the qnr gene was 21.13% (56/265), with the highest prevalence in markets (36.11%, 26/72), followed in farms (17.95%, 21/117), and slaughterhouses (10.53%, 9/76). Only the qnrS and qnrB genes were detected, and the prevalence rate of the qnrS gene (19.25%, 51/265) was higher than that of the qnrB gene (1.89%, 5/265). Whole genome sequencing identified 37 distinct AMR genes and 15 plasmid replicons, and the most frequent mutation in quinolone resistance determining regions was parC (T57S; 91.49%, 43/47). Meanwhile, four different qnrS and two qnrB genetic environments were discovered among 47 qnr-positive Salmonella strains. In total, 21.28% (10/47) of the strains were capable of conjugative transfer, and all were qnrS1-positive strains, with the majority of transferable plasmids being IncHI2 types (n = 4). Overall, the prevalence of qnr-positive Salmonella strains from chickens in China and their carriage of multiple resistance and virulence genes and transferable plasmids is a major concern, which calls for continuous surveillance of qnr-positive Salmonella and the development of measures to control its prevalence and transmission.IMPORTANCESalmonella is a common foodborne pathogen responsible for 155,000 deaths annually worldwide. Fluoroquinolones (FQs) are used as first-line drugs for the treatment of Salmonella infections in several countries and regions. However, the emergence and increasing prevalence of the FQ-resistant gene qnr in Salmonella isolated from chickens have been widely reported. Gaining insight into the genetic mechanisms of AMR genes in chicken could lead to the development of preventive measures to control and reduce the risk of drug resistance. In this study, we identified qnr-positive Salmonellae isolated from chickens in different regions of China and their AMR patterns and genome-wide characteristics, providing a theoretical basis for further control of their prevalence and transmission.
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Affiliation(s)
- Yang Chen
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lihui Liu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yali Guo
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinhua Chu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Bangjuan Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuxin Sui
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hanqi Wei
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Haihong Hao
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lingli Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Guyue Cheng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
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16
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Silva LC, Sanches MS, Guidone GHM, Montini VH, de Oliva BHD, do Nascimento AB, Galhardi LCF, Kobayashi RKT, Vespero EC, Rocha SPD. Clonal relationship, virulence genes, and antimicrobial resistance of Morganella morganii isolated from community-acquired infections and hospitalized patients: a neglected opportunistic pathogen. Int Microbiol 2024; 27:411-422. [PMID: 37479959 DOI: 10.1007/s10123-023-00400-x] [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: 05/10/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/23/2023]
Abstract
Morganella morganii is a bacterium belonging to the normal intestinal microbiota and the environment; however, in immunocompromised individuals, this bacterium can become an opportunistic pathogen, causing a series of diseases, both in hospitals and in the community, being urinary tract infections more prevalent. Therefore, the objective of this study was to evaluate the prevalence, virulence profile, and resistance to antimicrobials and the clonal relationship of isolates of urinary tract infections (UTI) caused by M. morganii, both in the hospital environment and in the community of the municipality of Londrina-PR, in southern Brazil, in order to better understand the mechanisms for the establishment of the disease caused by this bacterium. Our study showed that M. morganii presents a variety of virulence factors in the studied isolates. Hospital strains showed a higher prevalence for the virulence genes zapA, iutA, and fimH, while community strains showed a higher prevalence for the ireA and iutA genes. Hospital isolates showed greater resistance compared to community isolates, as well as a higher prevalence of multidrug-resistant (MDR) and extended-spectrum beta lactamase (ESBL)-producing isolates. Several M. morganii isolates from both sources showed high genetic similarity. The most prevalent plasmid incompatibility groups detected were FIB and I1, regardless of the isolation source. Thus, M. morganii isolates can accumulate virulence factors and antimicrobial resistance, making them a neglected opportunistic pathogen.
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Affiliation(s)
- Luana Carvalho Silva
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid PO-BOX 6001, 86051-980, Londrina, Paraná, Brazil
| | - Matheus Silva Sanches
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid PO-BOX 6001, 86051-980, Londrina, Paraná, Brazil
| | - Gustavo Henrique Migliorini Guidone
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid PO-BOX 6001, 86051-980, Londrina, Paraná, Brazil
| | - Victor Hugo Montini
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid PO-BOX 6001, 86051-980, Londrina, Paraná, Brazil
| | - Bruno Henrique Dias de Oliva
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid PO-BOX 6001, 86051-980, Londrina, Paraná, Brazil
| | - Arthur Bossi do Nascimento
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid PO-BOX 6001, 86051-980, Londrina, Paraná, Brazil
| | - Lígia Carla Faccin Galhardi
- Laboratory of Virology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Renata Katsuko Takayama Kobayashi
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Eliana Carolina Vespero
- Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, University Hospital of Londrina, State University of Londrina, Paraná, Brazil
| | - Sergio Paulo Dejato Rocha
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid PO-BOX 6001, 86051-980, Londrina, Paraná, Brazil.
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Tomeh R, Nemati A, Hashemi Tabar G, Tozzoli R, Badouei MA. Antimicrobial resistance, β-lactamase genotypes, and plasmid replicon types of Shiga toxin-producing Escherichia coli isolated from different animal hosts. J Appl Microbiol 2024; 135:lxae059. [PMID: 38467395 DOI: 10.1093/jambio/lxae059] [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: 01/16/2024] [Revised: 02/11/2024] [Accepted: 03/10/2024] [Indexed: 03/13/2024]
Abstract
AIMS The primary objective of this study was to analyze antimicrobial resistance (AMR), with a particular focus on β-lactamase genotypes and plasmid replicon types of Shiga toxin-producing Escherichia coli (STEC) strains originating from various animal hosts. METHODS AND RESULTS A total of 84 STEC strains were isolated from cattle (n = 32), sheep/goats (n = 26), pigeons (n = 20), and wild animals (n = 6) between 2010 and 2018 in various regions of Iran. The Kirby-Bauer susceptibility test and multiple polymerase chain reaction (PCR) panels were employed to elucidate the correlation between AMR and plasmid replicon types in STEC isolates. The predominant replicon types were IncFIC and IncFIB in cattle (46.8%), IncFIC in sheep/goats (46.1%), IncA/C in pigeons (90%), and IncP in wild animals (50%). STEC of serogroups O113, O26, and O111 harbored the IncFIB (100%), IncI1 (80%), and IncFIC + IncA/C (100%) plasmids, respectively. A remarkable AMR association was found between ciprofloxacin (100%), neomycin (68.7%), and tetracycline (61.7%) resistance with IncFIC; amoxicillin + clavulanic acid (88.8%) and tetracycline (61.7%) with IncA/C; ciprofloxacin (100%) with IncFIB; fosfomycin (85.7%) and sulfamethoxazole + trimethoprim (80%) with IncI1. IncI1 appeared in 83.3%, 50%, and 100% of the isolates harboring blaCTX-M, blaTEM, and blaOXA β-lactamase genes, respectively. CONCLUSIONS The emergence of O26/IncI1/blaCTX-M STEC in cattle farms poses a potential risk to public health.
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Affiliation(s)
- Rwida Tomeh
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Ali Nemati
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Gholamreza Hashemi Tabar
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Rosangela Tozzoli
- European Union Reference Laboratory for Escherichia coli, Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Mahdi Askari Badouei
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
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18
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Wu LT, Nguyen HTV, Ke SC, Lin YP, Pang YC, Guo MK, Chen CM. High Prevalence of Carbapenem-Resistant Enterobacterales Producing OXA-48 among Carbapenem-Resistant Isolates in a Regional Hospital in Central Taiwan. Jpn J Infect Dis 2024; 77:83-90. [PMID: 38030272 DOI: 10.7883/yoken.jjid.2023.213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
In response to the increasing number of carbapenem-resistant Enterobacterales (CRE), we investigated carbapenemase-producing Klebsiella pneumoniae and non-K. pneumoniae epidemiology and genetics. We collected 76 clinical Enterobacterales and 4 stool surveillance Escherichia coli isolates resistant to ertapenem or imipenem. Using polymerase chain reaction (PCR) and DNA sequencing, we assessed carbapenemases, extended-spectrum β-lactamases, and AmpC β-lactamases. Molecular typing via pulsed-field gel electrophoresis (PFGE) and conjugation experiments were conducted to examine resistance gene transfer. Among the 80 isolates, 96.2% harbored at least one carbapenemase gene, with blaOXA-48 in 87.5%. KPC-2 and IMP-8 carbapenemases were found in 15.0 and 22.5% of the isolates, respectively, with 27.5% having 2 or more carbapenemase genes. The PFGE analysis revealed the presence of diverse genotypes. PCR-based plasmid replicon typing identified IncA/C as the most prevalent type among K. pneumoniae isolates (26/29), and IncF and IncFIB among E. coli isolates (22/28). Conjugal transfer was successful for plasmids encoding OXA-48, CTX-M-3, CTX-M-14, CMY-2, and other β-lactamases, except the KPC-2 gene. In conclusion, our study highlights high carbapenemase prevalence in CRE, primarily OXA-48. Multiple carbapenemases within strains were common, and PFGE showed diverse patterns in these carbapenem-resistant isolates.
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Affiliation(s)
- Lii-Tzu Wu
- The Institute of Medical Science and Department of Microbiology, China Medical University Hospital, Taiwan
| | - Hong-Thuy Vy Nguyen
- The Institute of Biomedical Sciences College of Medicine, China Medical University, Taiwan
| | - Se-Chin Ke
- Infection Control Office, Tungs' Taichung MetroHarbor Hospital, Taiwan
- Department of Medical Technology, Jen-The Junior College of Medicine, Nursing and Management, Taiwan
| | - Yi-Pei Lin
- Department of Medical Research, Tungs' Taichung MetroHarbor Hospital, Taiwan
| | - Yi-Chun Pang
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, Taiwan
| | - Ming-Kai Guo
- The Institute of Medical Science and Department of Microbiology, China Medical University Hospital, Taiwan
| | - Chih-Ming Chen
- Division of Infectious Diseases, Department of Internal Medicine, Tungs' Taichung MetroHarbor Hospital, Taiwan
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19
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Martínez-Álvarez S, Châtre P, François P, Abdullahi IN, Simón C, Zarazaga M, Madec JY, Haenni M, Torres C. Unexpected role of pig nostrils in the clonal and plasmidic dissemination of extended-spectrum beta-lactamase-producing Escherichia coli at farm level. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116145. [PMID: 38460199 DOI: 10.1016/j.ecoenv.2024.116145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
The presence of methicillin-resistant or -susceptible S. aureus in pig nostrils has been known for a long time, but the occurrence of extended-spectrum beta-lactamase (ESBL)-producing E. coli has hardly been investigated. Here, we collected 25 E. coli recovered from nasal samples of 40 pigs/10 farmers of four farms. Nine ESBL-producing isolates belonging to ST48, ST117, ST847, ST5440, ST14914 and ST10 were retrieved from seven pigs. All blaESBL genes (blaCTX-M-32,blaCTX-M-14,blaCTX-M-1,blaCTX-M-65, and blaSHV-12) were horizontally transferable by conjugation through plasmids belonging to IncI1 (n=3), IncX1 (n=3) and IncHI2 (n=1) types. IncI1-plasmids displayed different genetic environments: i) IS26-blaSHV-12-deoR-IS26, ii) wbuC-blaCTX-M-32-ISKpn26 (IS5), and iii) IS930-blaCTX-M-14-IS26. The IncHI2-plasmid contained the genetic environment IS903-blaCTX-M-65-fipA with multiple resistance genes associated either to: a) Tn21-like transposon harbouring genes conferring aminoglycosides/beta-lactams/chloramphenicol/macrolides resistance located on two atypical class 1 integrons with an embedded ΔTn5393; or b) Tn1721-derived transposon displaying an atypical class 1 integron harbouring aadA2-arr3-cmlA5-blaOXA-10-aadA24-dfrA14, preceding the genetic platform IS26-blaTEM-95-tet(A)-lysR-floR-virD2-ISVsa3-IS3075-IS26-qnrS1, as well as the tellurite resistance module. Other plasmids harbouring clinically relevant genes were detected, such as a ColE-type plasmid carrying the mcr-4.5 gene. Chromosomally encoded genes (fosA7) or integrons (intI1-dfrA1-aadA1-qacE-sul1/intI1-IS15-dfrA1-aadA2) were also identified. Finally, an IncY plasmid harbouring a class 2 integron (intI2-dfrA1-sat2-aadA1-qacL-IS406-sul3) was detected but not associated with a blaESBL gene. Our results evidence that pig nostrils might favour the spread of ESBL-E. coli and mcr-mediated colistin-resistance. Therefore, enhanced monitoring should be considered, especially in a sector where close contact between animals in intensive farming increases the risk of spreading antimicrobial resistance.
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Affiliation(s)
- Sandra Martínez-Álvarez
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Pierre Châtre
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Pauline François
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Carmen Simón
- Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain.
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20
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Wahl A, Fischer MA, Klaper K, Müller A, Borgmann S, Friesen J, Hunfeld KP, Ilmberger A, Kolbe-Busch S, Kresken M, Lippmann N, Lübbert C, Marschner M, Neumann B, Pfennigwerth N, Probst-Kepper M, Rödel J, Schulze MH, Zautner AE, Werner G, Pfeifer Y. Presence of hypervirulence-associated determinants in Klebsiella pneumoniae from hospitalised patients in Germany. Int J Med Microbiol 2024; 314:151601. [PMID: 38359735 DOI: 10.1016/j.ijmm.2024.151601] [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: 10/13/2023] [Revised: 12/15/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Klebsiella (K.) pneumoniae is a ubiquitous Gram-negative bacterium and a common coloniser of animals and humans. Today, K. pneumoniae is one of the most persistent nosocomial pathogens worldwide and poses a severe threat/burden to public health by causing urinary tract infections, pneumonia and bloodstream infections. Infections mainly affect immunocompromised individuals and hospitalised patients. In recent years, a new type of K. pneumoniae has emerged associated with community-acquired infections such as pyogenic liver abscess in otherwise healthy individuals and is therefore termed hypervirulent K. pneumoniae (hvKp). The aim of this study was the characterisation of K. pneumoniae isolates with properties of hypervirulence from Germany. METHODS A set of 62 potentially hypervirulent K. pneumoniae isolates from human patients was compiled. Inclusion criteria were the presence of at least one determinant that has been previously associated with hypervirulence: (I) clinical manifestation, (II) a positive string test as a marker for hypermucoviscosity, and (III) presence of virulence associated genes rmpA and/or rmpA2 and/or magA. Phenotypic characterisation of the isolates included antimicrobial resistance testing by broth microdilution. Whole genome sequencing (WGS) was performed using Illumina® MiSeq/NextSeq to investigate the genetic repertoire such as multi-locus sequence types (ST), capsule types (K), further virulence associated genes and resistance genes of the collected isolates. For selected isolates long-read sequencing was applied and plasmid sequences with resistance and virulence determinants were compared. RESULTS WGS analyses confirmed presence of several signature genes for hvKp. Among them, the most prevalent were the siderophore loci iuc and ybt and the capsule regulator genes rmpA and rmpA2. The most dominant ST among the hvKp isolates were ST395 capsule type K2 and ST395 capsule type K5; both have been described previously and were confirmed by our data as multidrug-resistant (MDR) isolates. ST23 capsule type K1 was the second most abundant ST in this study; this ST has been described as commonly associated with hypervirulence. In general, resistance to beta-lactams caused by the production of extended-spectrum beta-lactamases (ESBL) and carbapenemases was observed frequently in our isolates, confirming the threatening rise of MDR-hvKp strains. CONCLUSIONS Our study results show that K. pneumoniae strains that carry several determinants of hypervirulence are present for many years in Germany. The detection of carbapenemase genes and hypervirulence associated genes on the same plasmid is highly problematic and requires intensified screening and molecular surveillance. However, the non-uniform definition of hvKp complicates their detection. Testing for hypermucoviscosity alone is not specific enough to identify hvKp. Thus, we suggest that the classification of hvKp should be applied to isolates that not only fulfil phenotypical criteria (severe clinical manifestations, hypermucoviscosity) but also (I) the presence of at least two virulence loci e.g. iuc and ybt, and (II) the presence of rmpA and/or rmpA2.
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Affiliation(s)
- Anika Wahl
- Robert Koch Institute, Division of Infectious Diseases, Department of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Martin A Fischer
- Robert Koch Institute, Division of Infectious Diseases, Department of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Kathleen Klaper
- Robert Koch Institute, Department of Sexually transmitted bacterial Pathogens (STI) and HIV, Berlin, Germany
| | - Annelie Müller
- Robert Koch Institute, Division of Infectious Diseases, Department of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Stefan Borgmann
- Klinikum Ingolstadt, Department of Infectious Diseases and Infection Control, Ingolstadt, Germany
| | | | - Klaus-Peter Hunfeld
- Institute for Laboratory Medicine, Microbiology & Infection Control, Northwest Medical Centre, Medical Faculty, Goethe University, Frankfurt am Main, Germany
| | | | - Susanne Kolbe-Busch
- Institute of Hygiene, Hospital Epidemiology and Environmental Medicine, Leipzig University Medical Center, Leipzig, Germany; Interdisciplinary Center for Infectious Diseases, Leipzig University Medical Center, Leipzig, Germany
| | - Michael Kresken
- Paul-Ehrlich-Gesellschaft für Infektionstherapie e. V., Cologne, Germany
| | - Norman Lippmann
- Institute for Medical Microbiology and Virology, University Hospital of Leipzig, Leipzig, Germany
| | - Christoph Lübbert
- Interdisciplinary Center for Infectious Diseases, Leipzig University Medical Center, Leipzig, Germany; Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Leipzig University Medical Center, Leipzig, Germany
| | | | - Bernd Neumann
- Institute of Clinical Microbiology, Infectious Diseases and Infection Control, Paracelsus Medical University, Nuremberg General Hospital, Nuremberg, Germany
| | - Niels Pfennigwerth
- German National Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | | | - Jürgen Rödel
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Marco H Schulze
- Department for Infection Control and Infectious Diseases, University Medical Center Goettingen, Goettingen, Germany
| | - Andreas E Zautner
- Institute of Medical Microbiology and Hospital Hygiene, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany; Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Guido Werner
- Robert Koch Institute, Division of Infectious Diseases, Department of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Yvonne Pfeifer
- Robert Koch Institute, Division of Infectious Diseases, Department of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany.
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Addis E, Unali I, Bertoncelli A, Ventura A, Cecchetto R, Mazzariol A. Different OXA-Carbapenemases in Genetically Unrelated Klebsiella pneumoniae Strains Isolated in a North Italian Hospital During Multidrug Resistance Screening. Microb Drug Resist 2024; 30:127-133. [PMID: 38165645 DOI: 10.1089/mdr.2023.0134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024] Open
Abstract
Klebsiella pneumoniae is one of the main opportunistic pathogens that cause a broad spectrum of diseases with increasingly frequent acquisition of resistance to antibiotics, namely carbapenems. This study focused on the characterization of 23 OXA-48-like carbapenemase-producing K. pneumoniae isolates using phenotypic and molecular tests. Phenotypic determination of the presence of β-lactamases was performed using the extended-spectrum beta-lactamase (ESBL) NP test, and phenotypic determination of the presence of carbapenemase was based on the Carba NP test. Antimicrobial susceptibility tests were performed to assess the resistance against carbapenems. Molecular characterization of ESBL genes and carbapenemase genes (blaOXA-48, blaKPC, blaVIM, and blaNDM) was performed using polymerase chain reaction (PCR) techniques. In addition, K. pneumoniae strains were analyzed for their relatedness using multilocus sequence typing PCR analysis based on the Institut Pasteur protocol, which produces allelic profiles that contain their evolutionary and geographic pattern. Following further Sanger sequencing of the blaOXA-48 genes, no genetic mutations were found. Some OXA-48-producing K. pneumoniae isolates coharbored blaKPC, blaNDM, and blaVIM genes, which encode other carbapenemases that can hydrolyze carbapenem antibiotics. The final part of the study focused on the characterization of the plasmid profiles of all isolates to better understand the spreading of the IncL/M blaOXA-48 plasmid gene. The plasmid profile also revealed other incompatibility groups, suggesting that other plasmid genes are spreading in K. pneumoniae isolates, which can coharbor and spread different carbapenemases simultaneously.
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Affiliation(s)
- Elena Addis
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Ilaria Unali
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Anna Bertoncelli
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Anna Ventura
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Riccardo Cecchetto
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Annarita Mazzariol
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
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Yu MK, Fogarty EC, Eren AM. Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess. Nat Microbiol 2024; 9:830-847. [PMID: 38443576 PMCID: PMC10914615 DOI: 10.1038/s41564-024-01610-3] [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: 07/21/2022] [Accepted: 01/17/2024] [Indexed: 03/07/2024]
Abstract
Plasmids alter microbial evolution and lifestyles by mobilizing genes that often confer fitness in changing environments across clades. Yet our ecological and evolutionary understanding of naturally occurring plasmids is far from complete. Here we developed a machine-learning model, PlasX, which identified 68,350 non-redundant plasmids across human gut metagenomes and organized them into 1,169 evolutionarily cohesive 'plasmid systems' using our sequence containment-aware network-partitioning algorithm, MobMess. Individual plasmids were often country specific, yet most plasmid systems spanned across geographically distinct human populations. Cargo genes in plasmid systems included well-known determinants of fitness, such as antibiotic resistance, but also many others including enzymes involved in the biosynthesis of essential nutrients and modification of transfer RNAs, revealing a wide repertoire of likely fitness determinants in complex environments. Our study introduces computational tools to recognize and organize plasmids, and uncovers the ecological and evolutionary patterns of diverse plasmids in naturally occurring habitats through plasmid systems.
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Affiliation(s)
- Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL, USA.
| | - Emily C Fogarty
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee On Microbiology, University of Chicago, Chicago, IL, USA
| | - A Murat Eren
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany.
- Marine 'Omics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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23
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Silva-Sánchez J, Duran-Bedolla J, Lozano L, Reyna-Flores F, Barrios-Camacho H. Molecular characterization of Escherichia coli producing extended-spectrum β-lactamase CTX-M-14 and CTX-M-28 in Mexico. Braz J Microbiol 2024; 55:309-314. [PMID: 37978118 PMCID: PMC10920525 DOI: 10.1007/s42770-023-01183-z] [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: 06/22/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023] Open
Abstract
The spread of ESBL-producing Escherichia coli has constantly increased in both clinical and community infections. Actually, the main ESBL reported is the CTX-M family, which is widely disseminated between the Enterobacteriaceae family. The epidemiology of the CTX-M family shows the CTX-M-15 variant dominating worldwide, followed by CTX-M-14 and CTX-M-27. The specific ESBL-producing E. coli clones included mainly the sequence types ST131, ST405, and ST648. In this report, we present the molecular characterization of ESBL-producing E. coli clinical isolates from eight hospitals in Mexico. From a collection of 66 isolates, 39 (59%) were identified as blaCTX-M-14 and blaCTX-M-27 belonging to the group CTX-M-9. We identified 25 (38%) isolates, producing blaCTX-M-28 belonging to the group CTX-M-1. blaCTX-M-2 and blaTEM-55 were identified in one isolate, respectively. Fourteen isolates (21%) were positive for blaCTX-M-14 (13%) and blaCTX-M-28 (7.3%) that were selected for further analyses; the antimicrobial susceptibility showed resistance to ampicillin (> 256 µg/mL), cefotaxime (> 256 µg/mL), cefepime (> 64 µg/mL), and ceftazidime (16 µg/mL). The ResFinder analysis showed the presence of the antimicrobial resistance genes aacA4, aadA5, aac(3)lla, sul1, dfrA17, tet(A), cmlA1, and blaTEM-1B. PlasmidFinder analysis identified in all the isolates the replicons IncFIB, which were confirmed by PCR replicon typing. The MLST analysis identified isolates belonging to ST131, ST167, ST405, and ST648. The ISEcp1B genetic element was found at 250 pb upstream of blaCTX-M-14 and flanked by the IS903 genetic element at 35 pb downstream. The IS1380-like element ISEc9 family transposase was identified at 250 pb upstream of blaCTX-M-14 and flanked downstream by the IS5/IS1182 at 80 pb. Our study highlights the significant prevalence of CTX-M-14 and CTX-M-28 enzymes as the second-most common ESBL-producing E. coli among isolates in Mexican hospitals. The identification of specific sequence types in different regions provides valuable insights into the correlation between ESBL and E. coli strains. This contribution to understanding their epidemiology and potential transmission routes is crucial for developing effective strategies to mitigate the spread of ESBL-producing E. coli in healthcare settings.
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Affiliation(s)
- Jesús Silva-Sánchez
- Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, Mexico
| | - Josefina Duran-Bedolla
- Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, Mexico
| | - Luis Lozano
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Fernando Reyna-Flores
- Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, Mexico
| | - Humberto Barrios-Camacho
- Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, Mexico.
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24
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Karaman E, Çiçek AÇ, Şemen V, Şaban Beriş F. Characterization of resistance genes and replicon typing in Carbapenem-resistant Klebsiella pneumoniae strains. Ann Clin Microbiol Antimicrob 2024; 23:19. [PMID: 38402160 PMCID: PMC10893597 DOI: 10.1186/s12941-024-00672-9] [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: 12/12/2023] [Accepted: 01/26/2024] [Indexed: 02/26/2024] Open
Abstract
OBJECTIVE In our study, K. pneumoniae strains (non-susceptible to carbapenem) (n = 60) were obtained from various clinical samples from Rize State Hospital between 2015 and 2017 and it is aimed to identify antibiotic resistance genes and replicon typing. METHODS Antibiotic susceptibility tests of the strains were performed with Kirby-Bauer disk diffusion test and the Vitek-2 automated system (BioMerieux, France). Antibiotic resistance genes and replicon typing was characterized by PCR method. RESULTS It was determined that K. pneumaniae isolates were mostly isolated from the samples of the intensive care unit. All of the K. pneumoniae strains examined in this study were found to be ampicillin/sulbactam and ertapenem resistant but colistin susceptible. Amoxacillin/clavulonic acid resistance was detected at 98.14% of strains. The blaOXA-48 gene was mostly detected in isolates. The most common type of plasmid was I1 and 3 different plasmid types were found in five different strains together. CONCLUSION This study also shows that the distribution of NDM-1 and OXA-48 carbapenemases has increased since the first co-display in Türkiye and that IncHI1 is the first record in our country. This study provides an overview of the major plasmid families occurring in multiple antibiotic-resistant strains of K. pneumoniae. To our knowledge, this study represents the first report of IncHI1 record in Türkiye.
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Affiliation(s)
- Esin Karaman
- Faculty of Arts&Sciences, Department of Biology, Recep Tayyip Erdogan University, Rize, Turkey
| | - Ayşegül Çopur Çiçek
- Faculty of Medicine, Department of Medical Microbiology, İstanbul Medipol University, İstanbul, Turkey
| | - Vicdan Şemen
- Department of Microbiology, Sakarya Yenikent State Hospital, Sakarya, Turkey
| | - Fatih Şaban Beriş
- Faculty of Arts&Sciences, Department of Biology, Recep Tayyip Erdogan University, Rize, Turkey.
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Kon H, Lurie-Weinberger MN, Lugassy C, Chen D, Schechner V, Schwaber MJ, Hussein K, Alon T, Tarabeia J, Hamo M, Firan I, Aboalhega W, Lomansov E, Mendelsohn S, Keren-Paz A, Carmeli Y. Use of Fourier-transform infrared spectroscopy for real-time outbreak investigation of OXA-48-producing Escherichia coli. J Antimicrob Chemother 2024; 79:349-353. [PMID: 38101944 DOI: 10.1093/jac/dkad387] [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: 10/26/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Efficient infection control during carbapenem-resistant Enterobacterales outbreaks demands rapid and simple techniques for outbreak investigations. WGS, the current gold standard for outbreak identification, is expensive, time-consuming and requires a high level of expertise. Fourier-transform infrared (FTIR) spectroscopy (IR Biotyper) is a rapid typing method based on infrared radiation applied to samples, which provides a highly specific absorption spectrum. OBJECTIVES To investigate an outbreak of OXA-48-producing Escherichia coli in real-time using FTIR and subsequently compare the results with WGS. METHODS Twenty-one isolates were collected during a nosocomial outbreak, and identification and antibiotic susceptibilities were confirmed by VITEK®2. FTIR was conducted for all isolates, and nine representative isolates were sequenced. RESULTS FTIR was able to correctly determine the clonal relatedness of the isolates and to identify the outbreak cluster, as confirmed by WGS. By WGS, isolates in the main FTIR cluster belonged to the same MLST type and core-genome MLST type, and they harboured similar plasmids and resistance genes, whereas the singletons external to the FTIR cluster had different genetic content. CONCLUSIONS FTIR can operate as a rapid, efficient and reliable first-line tool for outbreak investigations during a real-time ongoing E. coli outbreak, which can contribute to limiting the spread of pathogens.
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Affiliation(s)
- Hadas Kon
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv, Israel
| | - Mor N Lurie-Weinberger
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv, Israel
| | - Carmela Lugassy
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv, Israel
| | - Dafna Chen
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv, Israel
| | - Vered Schechner
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv, Israel
- School of Public Health, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Mitchell J Schwaber
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv, Israel
| | - Khetam Hussein
- Infection Control Unit, Rambam Health Care Campus, Haifa, Israel
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Tamar Alon
- Infection Control Unit, Rambam Health Care Campus, Haifa, Israel
| | - Jalal Tarabeia
- Infection Control Unit, Rambam Health Care Campus, Haifa, Israel
- Nursing Faculty, Max Stern Yezreel Valley College, Emek Yezreel, Israel
| | - Moran Hamo
- Infection Control Unit, Rambam Health Care Campus, Haifa, Israel
| | - Ibraheem Firan
- Infection Control Unit, Rambam Health Care Campus, Haifa, Israel
| | - Worood Aboalhega
- Infection Control Unit, Rambam Health Care Campus, Haifa, Israel
| | - Elena Lomansov
- Infection Control Unit, Rambam Health Care Campus, Haifa, Israel
| | - Sigal Mendelsohn
- Microbiology Laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Alona Keren-Paz
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv, Israel
| | - Yehuda Carmeli
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [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: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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27
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Song H, Zou S, Huang Y, Jian C, Liu W, Tian L, Gong L, Chen Z, Sun Z, Wang Y. Salmonella Typhimurium with Eight Tandem Copies of blaNDM-1 on a HI2 Plasmid. Microorganisms 2023; 12:20. [PMID: 38257847 PMCID: PMC10819877 DOI: 10.3390/microorganisms12010020] [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: 10/22/2023] [Revised: 12/09/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Carbapenem-resistant Salmonella has recently aroused increasing attention. In this study, a total of four sequence type 36 Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) isolates were consecutively isolated from an 11-month-old female patient with a gastrointestinal infection, of which one was sensitive to carbapenems and three were resistant to carbapenems. Via antibiotic susceptibility testing, a carbapenemases screening test, plasmid conjugation experiments, Illumina short-reads, and PacBio HiFi sequencing, we found that all four S. Typhimurium isolates contained a blaCTX-M-14-positive IncI1 plasmid. One carbapenem-sensitive S. Typhimurium isolate then obtained an IncHI2 plasmid carrying blaNDM-1 and an IncP plasmid without any resistance genes during the disease progression. The blaNDM-1 gene was located on a new 30 kb multiple drug resistance region, which is flanked by IS26 and TnAs2, respectively. In addition, the ST_F0903R isolate contained eight tandem copies of the ISCR1 unit (ISCR1-dsbD-trpF-ble-blaNDM-1-ISAba125Δ1), but an increase in MICs to carbapenems was not observed. Our work further provided evidence of the rapid spread and amplification of blaNDM-1 through plasmid. Prompting the recognition of carbapenem-resistant Enterobacterales and the initiation of appropriate infection control measures are essential to avoid the spread of these organisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.S.); (S.Z.); (Y.H.); (C.J.); (W.L.); (L.T.); (L.G.); (Z.C.); (Y.W.)
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28
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Xedzro C, Shimamoto T, Yu L, Zuo H, Sugawara Y, Sugai M, Shimamoto T. Emergence of colistin-resistant Enterobacter cloacae and Raoultella ornithinolytica carrying the phosphoethanolamine transferase gene, mcr-9, derived from vegetables in Japan. Microbiol Spectr 2023; 11:e0106323. [PMID: 37909761 PMCID: PMC10714742 DOI: 10.1128/spectrum.01063-23] [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: 03/13/2023] [Accepted: 09/17/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Plasmid-mediated mobile colistin-resistance genes have been recognized as a global threat because they jeopardize the efficacy of colistin in therapeutic practice. Here, we described the genetic features of two mcr-9.1-carrying Gram-negative bacteria with a colistin-resistant phenotype derived from vegetables in Japan. The colistin-resistant mcr-9.1, which has never been detected in vegetables, was located on a large plasmid in Enterobacter cloacae CST17-2 and Raoultella ornithinolytica CST129-1, suggesting a high chance of horizontal gene transfer. To the best of our knowledge, this is the first report of mcr-9 in R. ornithinolytica. This study indicates that fresh vegetables might be a potential source for the transmission of mcr-9 genes encoding resistance to frontline (colistin) and clinically relevant antimicrobials. The study also provides additional consideration for colistin use and the relevance of routine surveillance in epidemiological perspective to curb the continuous spread of mcr alleles.
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Affiliation(s)
- Christian Xedzro
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Toshi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Liansheng Yu
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Hui Zuo
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Yo Sugawara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Tadashi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
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Xedzro C, Shimamoto T, Shimamoto T. Predominance of Multidrug-Resistant Gram-Negative Bacteria Isolated from Supermarket Retail Seafood in Japan. Microorganisms 2023; 11:2935. [PMID: 38138079 PMCID: PMC10745518 DOI: 10.3390/microorganisms11122935] [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: 11/08/2023] [Revised: 11/20/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
Reports have documented antimicrobial usage in aquaculture, and the aquatic ecosystem can be considered a genetic storage site for antibiotic-resistant bacteria. This study assessed the prevalence of antimicrobial resistance (AMR) among Gram-negative bacteria recovered from retail seafood in Hiroshima, Japan. A total of 412 bacteria were isolated and screened for the presence of β-lactamases, acquired carbapenemases, and mobile colistin-resistance (mcr) genes. Forty-five (10.9%) isolates were dominated by Morganella (28%), Proteus (22%), Aeromonas (14%), Citrobacter (8%), and Escherichia (8%) and carried AMR genes. The identified AMR genes included those encoded in integrons (19), aac(6՛)-Ib (11), blaTEM-1 (7), blaCTX-M-like (12), blaCTX-M-65 (2), blaSHV-12 (1), blaSHV-27 (1), blaOXA-10 (1), blaOXA-2 (1), and mcr (2). The most common clinical resistances were against ampicillin, colistin, sulfamethoxazole/trimethoprim, tetracycline, and ciprofloxacin. Multidrug resistance (MDR) occurred in 27 (60%) AMR isolates, and multiple antibiotic resistance indices ranged from 0.2 to 0.8. A conjugation experiment showed that 10 of the 11 selected MDR strains harbored conjugable plasmids, although PCR-based replicon typing described seven strains as untypable. IncF replicon was identified in MDR extended-spectrum β-lactamase-producing Escherichia coli of the pathogenic B2 phylogroup. Our findings suggest that retail seafood harbors MDR bacteria of human interest that require strict resistance surveillance in the seafood production continuum.
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Affiliation(s)
| | | | - Tadashi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan; (C.X.); (T.S.)
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30
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Duran-Bedolla J, Garza-Ramos U, Silva-Sánchez J, Lozano L, Reyna-Flores F, Sánchez-Pérez A, Barrios-Camacho H. Genetic characterization of plasmid-mediated fluoroquinolone efflux pump QepA among ESBL-producing Escherichia coli isolates in Mexico. Braz J Microbiol 2023; 54:2791-2797. [PMID: 37702924 PMCID: PMC10689307 DOI: 10.1007/s42770-023-01115-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/23/2023] [Indexed: 09/14/2023] Open
Abstract
Antimicrobial resistance is a major global public health problem, with fluoroquinolone-resistant strains of Escherichia coli posing a significant threat. This study examines the genetic characterization of ESBL-producing E. coli isolates in Mexican hospitals, which are resistant to both cephalosporins and fluoroquinolones. A total of 23 ESBL-producing E. coli isolates were found to be positive for the qepA gene, which confers resistance to fluoroquinolones. These isolates exhibited drug resistance phenotypes and belonged to specific sequence types and phylogenetic groups. The genetic context of the qepA gene was identified in a novel genetic context flanked by IS26 sequences. Mating experiments showed the co-transfer of qepA1 and chrA determinants alongside blaCTX-M-15 genes, emphasizing the potential for these genetic structures to spread among Enterobacterales. The emergence of multidrug-resistant Gram-negative bacteria carrying these resistance genes is a significant clinical concern for public healthcare systems.
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Affiliation(s)
- Josefina Duran-Bedolla
- Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán. C.P, 62100, Cuernavaca, Morelos, México
| | - Ulises Garza-Ramos
- Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán. C.P, 62100, Cuernavaca, Morelos, México
| | - Jesús Silva-Sánchez
- Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán. C.P, 62100, Cuernavaca, Morelos, México
| | - Luis Lozano
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Fernando Reyna-Flores
- Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán. C.P, 62100, Cuernavaca, Morelos, México
| | - Alejandro Sánchez-Pérez
- Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán. C.P, 62100, Cuernavaca, Morelos, México
| | - Humberto Barrios-Camacho
- Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán. C.P, 62100, Cuernavaca, Morelos, México.
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31
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Moussa J, Nassour E, Tahan E, El Chaar M, Jisr T, Tokajian S. Carbapenem resistance determinants and their transmissibility among clinically isolated Enterobacterales in Lebanon. J Infect Public Health 2023; 16:1947-1953. [PMID: 37871361 DOI: 10.1016/j.jiph.2023.10.003] [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: 03/06/2023] [Revised: 06/13/2023] [Accepted: 10/02/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND The occurrence of carbapenem-resistant bacterial infections has increased significantly over the years with Gram-negative bacteria exhibiting the broadest resistance range. In this study we aimed to investigate the genomic characteristics of clinical carbapenem-resistant Enterobacterales (CRE). METHODS Seventeen representative multi-drug resistant (MDR) isolates from a hospital setting showing high level of resistance to carbapenems (ertapenem, meropenem and imipenem) were chosen for further characterization through whole-genome sequencing. Resistance mechanisms and transferability of plasmids carrying carbapenemase-encoding genes were also determined in silico and through conjugative mating assays. RESULTS We detected 18 different β-lactamases, including four carbapenemases (blaNDM-1, blaNDM-5, blaNDM-7, blaOXA-48) on plasmids with different Inc groups. The combined results from PBRT and in silico replicon typing revealed 20 different replicons linked to plasmids ranging in size between 80 and 200 kb. The most prevalent Inc groups were IncFIB(K) and IncM. OXA-48, detected on 76-kb IncM1 conjugable plasmid, was the most common carbapenemase. We also detected other conjugative plasmids with different carbapenemases confirming the role of horizontal gene transfer in the dissemination of antimicrobial resistance genes. CONCLUSION Our findings verified the continuing spread of carbapenemases in Enterobacterales and revealed the types of mobile elements circulating in a hospital setting and contributing to the spread of resistance determinants. The occurrence and transmission of plasmids carrying carbapenemase-encoding genes call for strengthening active surveillance and prevention efforts to control antimicrobial resistance dissemination in healthcare settings.
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Affiliation(s)
- Jennifer Moussa
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos 1401, Lebanon
| | - Elie Nassour
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos 1401, Lebanon
| | - Elio Tahan
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos 1401, Lebanon
| | - Mira El Chaar
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Tamima Jisr
- Laboratory Medicine Department, Makassed General Hospital, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos 1401, Lebanon.
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Naha S, Basak P, Sands K, Milton R, Carvalho MJ, Mitra S, Bhattacharjee A, Sinha A, Mukherjee S, Saha B, Chattopadhyay P, Chakravorty PS, Nandy RK, Dutta S, Walsh TR, Basu S. Carriage and within-host diversity of mcr-1.1-harbouring Escherichia coli from pregnant mothers: inter- and intra-mother transmission dynamics of mcr-1.1. Emerg Microbes Infect 2023; 12:2278899. [PMID: 37929689 PMCID: PMC10773534 DOI: 10.1080/22221751.2023.2278899] [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: 06/11/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Exchange of antimicrobial resistance genes via mobile genetic elements occur in the gut which can be transferred from mother to neonate during birth. This study is the first to analyse transmissible colistin resistance gene, mcr, in pregnant mothers and neonates. Samples were collected from pregnant mothers (rectal) and septicaemic neonates (rectal and blood) and analysed for the presence of mcr, its transmissibility, genome diversity, and exchange of mcr between isolates within an individual and across different individuals (not necessarily mother-baby pairs). mcr-1.1 was detected in rectal samples of pregnant mothers (n = 10, 0.9%), but not in neonates. All mcr-positive mothers gave birth to healthy neonates from whom rectal specimen were not collected. Hence, the transmission of mcr between these mother-neonate pairs could not be studied. mcr-1.1 was noted only in Escherichia coli (phylogroup A & B1), and carried few resistance and virulence genes. Isolates belonged to diverse sequence types (n = 11) with two novel STs (ST12452, ST12455). mcr-1.1 was borne on conjugative IncHI2 bracketed between ISApl1 on Tn6630, and the plasmids exhibited similarities in sequences across the study isolates. Phylogenetic comparison showed that study isolates were related to mcr-positive isolates of animal origin from Southeast Asian countries. Spread of mcr-1.1 within this study occurred either via similar mcr-positive clones or similar mcr-bearing plasmids in mothers. Though this study could not build evidence for mother-baby transmission but the presence of such genes in the maternal specimen may enhance the chances of transmission to neonates.
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Affiliation(s)
- Sharmi Naha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Priyanka Basak
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Kirsty Sands
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
- Department of Zoology, Ineos Oxford Institute of Antimicrobial Research, University of Oxford, Oxford, UK
| | - Rebecca Milton
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
- Centre for Trials Research, Cardiff University, Cardiff, UK
| | - Maria J. Carvalho
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
- Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Shravani Mitra
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Amrita Bhattacharjee
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Anuradha Sinha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Suchandra Mukherjee
- Department of Neonatology, Institute of Post-Graduate and Medical Education & Research, Kolkata, India
| | - Bijan Saha
- Department of Neonatology, Institute of Post-Graduate and Medical Education & Research, Kolkata, India
| | - Pinaki Chattopadhyay
- Department of Neonatology, Institute of Post-Graduate and Medical Education & Research, Kolkata, India
| | - Partha Sarathi Chakravorty
- Department of Obstetrics & Gynecology, Institute of Post-Graduate and Medical Education & Research, Kolkata, India
| | - Ranjan Kumar Nandy
- 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
| | - Timothy R. Walsh
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
- Department of Zoology, Ineos Oxford Institute of Antimicrobial Research, University of Oxford, Oxford, UK
| | - Sulagna Basu
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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Grilo T, Freire S, Miguel B, Martins LN, Menezes MF, Nordmann P, Poirel L, Sousa MJR, Aires-de-Sousa M. Occurrence of plasmid-mediated fosfomycin resistance (fos genes) among Escherichia coli isolates, Portugal. J Glob Antimicrob Resist 2023; 35:342-346. [PMID: 37553021 DOI: 10.1016/j.jgar.2023.08.001] [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: 03/01/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
OBJECTIVES To evaluate the occurrence of plasmid-mediated fos genes among fosfomycin-resistant Escherichia coli isolates collected from patients in Lisbon, Portugal, and characterize the fos-positive strains. METHODS A total of 19 186 E. coli isolates were prospectively collected between April 2022 and January 2023 from inpatients and outpatients at a private laboratory in Lisbon. Fosfomycin resistance was initially assessed by semi-automated systems and further confirmed by the disc diffusion method. Resistant isolates were investigated for plasmid-mediated fos genes (fosA1-fosA10, fosC and fosL1-fosL2) and extended-spectrum beta-lactamases (ESBLs) by PCR and sequencing. Multilocus sequence typing was performed to evaluate the clonal relationship among fos-carrying isolates. RESULTS Out of the 19 186 E. coli isolates, 100 were fosfomycin-resistant (0.5%), out of which 15 carried a fosA-like gene (15%). The most prevalent fosfomycin-resistant determinant was fosA3 (n = 11), followed by fosA4 (n = 4). Among the 15 FosA-producing isolates, 10 co-produced an ESBL (67%), being either of CTX-M-15 (n = 8) or CTX-M-14 (n = 2) types. The fosA3 gene was carried on IncFIIA-, IncFIB-, and IncY-type plasmids, whereas fosA4 was always located on IncFIB-type plasmids. Most FosA4-producing isolates belonged to a single sequence type ST2161, whereas isolates carrying the fosA3 gene were distributed into nine distinct genetic backgrounds. CONCLUSION The prevalence of fosfomycin-resistant E. coli isolates is still low in Portugal. Notably, 15% of fosfomycin-resistant isolates harbour a transferable fosA gene, among which there is a high rate of ESBL producers, turning traditional empirical therapeutical options used in Portugal (fosfomycin and amoxicillin-clavulanic acid) ineffective.
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Affiliation(s)
- Teresa Grilo
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Samanta Freire
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Bruno Miguel
- Centro Medicina Laboratorial - Germano de Sousa, Lisboa, Portugal
| | | | - Maria Favila Menezes
- Centro Medicina Laboratorial - Germano de Sousa, Lisboa, Portugal; Hospital CUF Descobertas, Lisboa, Portugal
| | - Patrice Nordmann
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Maria José Rego Sousa
- Centro Medicina Laboratorial - Germano de Sousa, Lisboa, Portugal; Hospital CUF Descobertas, Lisboa, Portugal
| | - Marta Aires-de-Sousa
- Escola Superior de Saúde da Cruz Vermelha Portuguesa - Lisboa (ESSCVP-Lisboa), Lisboa, Portugal; Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
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Pan F, Chen P, Duan Y, Yu F, Weng W, Zhang H. Prevalence of intestinal colonization and nosocomial infection with carbapenem-resistant Enterobacteriales in children: a retrospective study. Front Public Health 2023; 11:1251609. [PMID: 38074706 PMCID: PMC10702246 DOI: 10.3389/fpubh.2023.1251609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/09/2023] [Indexed: 12/18/2023] Open
Abstract
Objective We investigated the epidemiological surveillance of the intestinal colonization and nosocomial infection of carbapenem-resistant Enterobacteriales (CRE) isolates from inpatients, which can provide the basis for developing effective prevention. Methods A total of 96 CRE strains were collected from 1,487 fecal samples of hospitalized children between January 2016 and June 2017, which were defined as the "CRE colonization" group. In total, 70 CRE clinical isolates were also randomly selected for the comparison analysis and defined as the "CRE infection" group. The antimicrobial susceptibility of all strains was determined by the microdilution broth method. Polymerase chain reaction (PCR) was used to analyze carbapenemase genes, plasmid typing, and integrons. Multilocus sequence typing was further used to determine clonal relatedness. Results In the "CRE colonization" group, Klebsiella pneumoniae was mostly detected with a rate of 42.7% (41/96), followed by Escherichia coli (34.4%, 33/96) and Enterobacter cloacae (15.6%, 15/96). The ST11 KPC-2 producer, ST8 NDM-5 producer, and ST45 NDM-1 producer were commonly present in carbapenem-resistant K. pneumoniae (CRKPN), carbapenem-resistant E. coli (CRECO), and carbapenem-resistant E. cloacae (CRECL) isolates, respectively. In the "CRE infection" group, 70% (49/70) of strains were K. pneumoniae, with 21.4% E. cloacae (15/70) and 5.7% E. coli (4/70). The ST15 OXA-232 producer and ST48 NDM-5 producer were frequently observed in CRKPN isolates, while the majority of NDM-1-producing CRECL isolates were assigned as ST45. Phylogenetic analysis showed that partial CRE isolates from intestinal colonization and nosocomial infection were closely related, especially for ST11 KPC-2-producing CRKPN and ST45 NDM-1-producing CRECL. Furthermore, plasmid typing demonstrated that IncF and IncFIB were the most prevalent plasmids in KPC-2 producers, while IncX3/IncX2 and ColE were widely spread in NDM producer and OXA-232 producer, respectively. Then, class 1 integron intergrase intI1 was positive in 74.0% (71/96) of the "CRE colonization" group and 52.9% (37/70) of the "CRE infection" group. Conclusion This study revealed that CRE strains from intestinal colonization and nosocomial infection showed a partial correlation in the prevalence of CRE, especially for ST11 KPC-2-producing CRKPN and ST45 NDM-1-producing CRECL. Therefore, before admission, long-term active screening of rectal colonization of CRE isolates should be emphasized.
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Affiliation(s)
- Fen Pan
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Yuxin Duan
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fangyuan Yu
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenhao Weng
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Das S, Mallick A, Barik M, Sarkar S, Saha P. The emergence of clonally diverse carbapenem-resistant Enterobacter cloacae complex in West Bengal, India: a dockyard of β-lactamases periling nosocomial infections. Int Microbiol 2023:10.1007/s10123-023-00451-0. [PMID: 37985632 DOI: 10.1007/s10123-023-00451-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023]
Abstract
Carbapenem-resistant Enterobacter cloacae complex (CRECC) constitutes a global public health threat challenging clinical treatment and infection control, especially in low- and middle-income countries such as India. We analyzed the antimicrobial susceptibility, major β-lactamase genes, plasmid profiles, and genetic relatedness to understand the molecular epidemiology of CRECC clinical isolates (n = 44) in West Bengal, India, during 2021-2022. The majority (> 55%) of the isolates were resistant to fluoroquinolones, aminoglycosides, and co-trimoxazole, even > 20% for tigecycline and > 35% were extensively drug-resistant. Co-β-lactamase production was categorized into twenty-seven types, importantly NDM (84%), OXA-48 (40%), TEM (61%), CTX-M (46%), OXA-1 (55%), and MIR (27%). The NDM-1 and OXA-181 were major variants with the first observations of NDM-24 and -29 variants in India. Wide-range of plasmids (2 to > 212 kb) were harbored by the β-lactamase-producing isolates: small (91%), medium (27%), large (9%), and mega (71%). IncX3, ColE1, and HI2 were noted in about 30% of isolates, while IncF and R were carried by < 20% of isolates. The clonally diverse CRECC isolates were noted to cause cross-infections, especially at superficial site, bloodstream, and urinary-tract. This is the first molecular surveillance on CRECC in India. The study isolates serve as the dockyard of NDM, TEM, and CTX-M harboring a wide range of plasmids. The outcomes of the study may strengthen local and national policies for infection prevention and control practices, clarifying the genetic diversity among CRECC. Extensive genomic study may further intersect the relationships between these different plasmids, especially with their sizes, types, and antibiotic resistance markers.
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Affiliation(s)
- Surojit Das
- Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India.
| | - Abhi Mallick
- Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Mili Barik
- Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Soma Sarkar
- Department of Microbiology at Nil Ratan Sirkar Medical College Hospital, Kolkata, West Bengal, India
- Department of Microbiology at Infectious Diseases & Beleghata General Hospital, Kolkata, West Bengal, India
| | - Puranjoy Saha
- Department of Microbiology, Malda Medical College and Hospital, Malda, West Bengal, India
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Avgere E, Zafeiridis C, Procter KA, Beloukas A, Giakkoupi P. Molecular Characterization of Escherichia coli Producing Extended-Spectrum ß-Lactamase and MCR-1 from Sick Pigs in a Greek Slaughterhouse. Antibiotics (Basel) 2023; 12:1625. [PMID: 37998827 PMCID: PMC10669062 DOI: 10.3390/antibiotics12111625] [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: 10/18/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/25/2023] Open
Abstract
The first prospective surveillance of ESBL and colistin-resistant Escherichia coli recovered from sick pigs from a slaughterhouse in Central Greece aimed to investigate the spread of relevant genetic elements. In February 2021, 25 E. coli isolates were subjected to antimicrobial susceptibility testing using disk diffusion and broth microdilution techniques. PCR screening was conducted to identify ESBLs and mcr genes. Additional assays, encompassing mating-out procedures, molecular typing utilizing Pulsed-Field Gel Electrophoresis, multilocus sequence typing analysis, and plasmid typing, were also conducted. A 40% prevalence of ESBLs and an 80% prevalence of MCR-1 were identified, with a co-occurrence rate of 32%. The predominant ESBL identified was CTX-M-3, followed by SHV-12. Resistance to colistin, chloramphenicol, cotrimoxazol, and ciprofloxacin was detected in twenty (80%), fifteen (60%), twelve (48%), and four (16%) isolates, respectively. All blaCTX-M-3 harboring plasmids were conjugative, belonging to the incompatibility group IncI1, and approximately 50 kb in size. Those carrying blaSHV-12 were also conjugative, classified into incompatibility group IncI2, and approximately 70 kb in size. The mcr-1 genes were predominantly located on conjugative plasmids associated with the IncX4 incompatibility group. Molecular typing of the ten concurrent ESBL and MCR-1 producers revealed seven multilocus sequence types. The heterogeneous population of E. coli isolates carrying resistant genes on constant plasmids implies that the dissemination of resistance genes is likely facilitated by horizontal plasmid transfer.
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Affiliation(s)
- Ermioni Avgere
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (E.A.); (K.A.P.); (A.B.)
| | - Christos Zafeiridis
- Public Health Policy Department, University of West Attica, 11521 Athens, Greece;
- Ministry of Rural Development and Food of Greece (General Directorate of Veterinary Services), Seconded National Expert to the European Commission (Directorate General of Health and Food Safety-Unit G4, Official Controls-Northern Ireland Liaison Team), Belfast BT96DR, UK
| | - Kassandra A. Procter
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (E.A.); (K.A.P.); (A.B.)
- National AIDS Reference Centre of Southern Greece, Department of Public Health Policy, University of West Attica, 11521 Athens, Greece
| | - Apostolos Beloukas
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (E.A.); (K.A.P.); (A.B.)
- National AIDS Reference Centre of Southern Greece, Department of Public Health Policy, University of West Attica, 11521 Athens, Greece
| | - Panagiota Giakkoupi
- Public Health Policy Department, University of West Attica, 11521 Athens, Greece;
- Laboratory for the Surveillance of Infectious Diseases-LSID, Department of Public Health Policy, University of West Attica, 11521 Athens, Greece
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Duran-Bedolla J, Rodríguez-Medina N, Dunn M, Mosqueda-García D, Barrios-Camacho H, Aguilar-Vera A, Aguilar-Vera E, Suárez-Rodríguez R, Ramírez-Trujillo JA, Garza-Ramos U. Plasmids of the incompatibility group FIB K occur in Klebsiella variicola from diverse ecological niches. Int Microbiol 2023; 26:917-927. [PMID: 36971854 DOI: 10.1007/s10123-023-00346-0] [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: 01/23/2023] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
Plasmids play a fundamental role in the evolution of bacteria by allowing them to adapt to different environments and acquire, through horizontal transfer, genes that confer resistance to different classes of antibiotics. Using the available in vitro and in silico plasmid typing systems, we analyzed a set of isolates and public genomes of K. variicola to study its plasmid diversity. The resistome, the plasmid multilocus sequence typing (pMLST), and molecular epidemiology using the MLST system were also studied. A high frequency of IncF plasmids from human isolates but lower frequency from plant isolates were found in our strain collection. In silico detection revealed 297 incompatibility (Inc) groups, but the IncFIBK (216/297) predominated in plasmids from human and environmental samples, followed by IncFIIK (89/297) and IncFIA/FIA(HI1) (75/297). These Inc groups were associated with clinically important ESBL (CTX-M-15), carbapenemases (KPC-2 and NDM-1), and colistin-resistant genes which were associated with major sequence types (ST): ST60, ST20, and ST10. In silico MOB typing showed 76% (311/404) of the genomes contained one or more of the six relaxase families with MOBF being most abundant. We identified untypeable plasmids carrying blaKPC-2, blaIMP-1, and blaSHV-187 but for which a relaxase was found; this may suggest that novel plasmid structures could be emerging in this bacterial species. The plasmid content in K. variicola has limited diversity, predominantly composed of IncFIBK plasmids dispersed in different STs. Plasmid detection using the replicon and MOB typing scheme provide a broader context of the plasmids in K. variicola. This study showed that whole-sequence-based typing provides current insights of the prevalence of plasmid types and their association with antimicrobial resistant genes in K. variicola obtained from humans and environmental niches.
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Affiliation(s)
- Josefina Duran-Bedolla
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Nadia Rodríguez-Medina
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Michael Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Dalila Mosqueda-García
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Humberto Barrios-Camacho
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Alejandro Aguilar-Vera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Edgar Aguilar-Vera
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Ramón Suárez-Rodríguez
- Laboratorio de Fisiología Molecular de Plantas, Centro de Investigación en Biotecnología (CEIB), Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - José Augusto Ramírez-Trujillo
- Laboratorio de Fisiología Molecular de Plantas, Centro de Investigación en Biotecnología (CEIB), Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Ulises Garza-Ramos
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México.
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Rahimzadeh M, Shahbazi S, Sabzi S, Habibi M, Asadi Karam MR. Antibiotic resistance and genetic diversity among Pseudomonas aeruginosa isolated from urinary tract infections in Iran. Future Microbiol 2023; 18:1171-1183. [PMID: 37882782 DOI: 10.2217/fmb-2023-0118] [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: 05/21/2023] [Accepted: 07/14/2023] [Indexed: 10/27/2023] Open
Abstract
Aims: To determine the antibiotic resistance and genetic diversity of Pseudomonas aeruginosa isolates. Methods: The antibiotic resistance, genetic diversity and the conjugate transformation among Pseudomonas aeruginosa collected from patients with urinary tract infection in Tehran, Iran, was investigated. Results: Antibiotic resistance against cefepime was seen in 51.74% of the isolates, followed by amikacin (47.76%). blaOXA-10 and blaVIM were the most prevalent extended-spectrum β-lactamase and metallo-β-lactamases genes, respectively. Five clusters (C1-C5) were obtained by pulse field gel electrophoresis and multilocus sequence typing revealed two strain types, ST235 and ST664. Conjugation detected blaOXA-48 and blaNDM genes were transferred to Escherichia coli K12. Conclusion: The resistance of P. aeruginosa to antibiotics is increasing, which highlights the need to determine the resistance patterns to design better treatment strategies.
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Affiliation(s)
- Mohammad Rahimzadeh
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, 13164, Iran
| | - Shahla Shahbazi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, 13164, Iran
| | - Samira Sabzi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, 13164, Iran
| | - Mehri Habibi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, 13164, Iran
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Kutlu HH, Dolapçı İ, Avcı M, Tekeli A. The emergence of Klebsiella pneumoniae sequence type 395 non-susceptible to carbapenems and colistin from Turkey. Indian J Med Microbiol 2023; 46:100419. [PMID: 37945113 DOI: 10.1016/j.ijmmb.2023.100419] [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: 08/04/2022] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 11/12/2023]
Abstract
PURPOSE OXA-48 producing Klebsiella pneumoniae is an emerging threat and outbreaks due to specific sequence types have been commonly reported. Here, we report an outbreak due to multidrug-resistant ST395 K. pneumoniae ST395. To the best of our knowledge, this is the first outbreak of K. pneumoniae ST395 harbouring blaOXA-48 genes in our country. METHODS The strains were characterized by antimicrobial susceptibility, extended-spectrum β-lactamase (ESBL) and carbapenemase production, plasmid-mediated colistin, high-level aminoglycoside, and quinolone resistance. Also multidrug efflux pumps and porin coding genes were investigated. Pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), wzi typing and plasmid analysis were used for the epidemiological relationships. RESULTS All strains were positive for blaOXA-48 with at least one of the β-lactamase genes (blaCTX-M, blaTEM, blaSHV) and harboured IncL plasmids. 16 of 20 (80%) isolates carried qnrA. All isolates were positive for aac(6')-1b, acrAB-tolC, ompK35, and ompK36 genes but none of them harboured 16s rRNA methyltransferase, mcr-1-5, qepA, oqxAB, and mdtK genes. All strains had the same PFGE pattern, that is, wzi type K2 and found to be ST395 with MLST. CONCLUSION The association of ST395 with OXA-48-producers could be an emerging threat for Turkey and continuous monitoring is crucial to prevent the spread of these powerful strains.
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Affiliation(s)
- Hüseyin Haydar Kutlu
- Department of Medical Microbiology, Faculty of Medicine, Usak University, Usak, Turkey.
| | - İştar Dolapçı
- Department of Medical Microbiology, Ankara University School of Medicine, Ankara, Turkey
| | - Meltem Avcı
- Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Usak University, Usak, Turkey
| | - Alper Tekeli
- Department of Medical Microbiology, Ankara University School of Medicine, Ankara, Turkey
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Subramani P, Menichincheri G, Pirolo M, Arcari G, Kudirkiene E, Polani R, Carattoli A, Damborg P, Guardabassi L. Genetic background of neomycin resistance in clinical Escherichia coli isolated from Danish pig farms. Appl Environ Microbiol 2023; 89:e0055923. [PMID: 37787538 PMCID: PMC10617424 DOI: 10.1128/aem.00559-23] [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: 04/04/2023] [Accepted: 07/28/2023] [Indexed: 10/04/2023] Open
Abstract
Neomycin is the first-choice antibiotic for the treatment of porcine enteritis caused by enterotoxigenic Escherichia coli. Resistance to this aminoglycoside is on the rise after the increased use of neomycin due to the ban on zinc oxide. We identified the neomycin resistance determinants and plasmid contents in a historical collection of 128 neomycin-resistant clinical E. coli isolates from Danish pig farms. All isolates were characterized by whole-genome sequencing and antimicrobial susceptibility testing, followed by conjugation experiments and long-read sequencing of eight selected representative strains. We detected 35 sequence types (STs) with ST100 being the most prevalent lineage (38.3%). Neomycin resistance was associated with two resistance genes, namely aph(3')-Ia and aph(3')-Ib, which were identified in 93% and 7% of the isolates, respectively. The aph(3')-Ia was found on different large conjugative plasmids belonging to IncI1α, which was present in 67.2% of the strains, on IncHI1, IncHI2, and IncN, as well as on a multicopy ColRNAI plasmid. All these plasmids except ColRNAI carried genes encoding resistance to other antimicrobials or heavy metals, highlighting the risk of co-selection. The aph(3')-Ib gene occurred on a 19 kb chimeric, mobilizable plasmid that contained elements tracing back its origin to distantly related genera. While aph(3')-Ia was flanked by either Tn903 or Tn4352 derivatives, no clear association was observed between aph(3')-Ib and mobile genetic elements. In conclusion, the spread of neomycin resistance in porcine clinical E. coli is driven by two resistance determinants located on distinct plasmid scaffolds circulating within a highly diverse population dominated by ST100. IMPORTANCE Neomycin is the first-choice antibiotic for the management of Escherichia coli enteritis in pigs. This work shows that aph(3')-Ia and to a lesser extent aph(3')-Ib are responsible for the spread of neomycin resistance that has been recently observed among pig clinical isolates and elucidates the mechanisms of dissemination of these two resistance determinants. The aph(3')-Ia gene is located on different conjugative plasmid scaffolds and is associated with two distinct transposable elements (Tn903 and Tn4352) that contributed to its spread. The diffusion of aph(3')-Ib is mediated by a small non-conjugative, mobilizable chimeric plasmid that likely derived from distantly related members of the Pseudomonadota phylum and was not associated with any detectable mobile genetic element. Although the spread of neomycin resistance is largely attributable to horizontal transfer, both resistance determinants have been acquired by a predominant lineage (ST100) associated with enterotoxigenic E. coli, which accounted for approximately one-third of the strains.
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Affiliation(s)
- Prabha Subramani
- Department of Veterinary and Animal Sciences, Section for Veterinary Clinical Microbiology, University of Copenhagen, Frederiksberg C, Denmark
- Department of Molecular Medicine Sapienza, University of Rome, Rome, Italy
| | - Gaia Menichincheri
- Department of Molecular Medicine Sapienza, University of Rome, Rome, Italy
| | - Mattia Pirolo
- Department of Veterinary and Animal Sciences, Section for Veterinary Clinical Microbiology, University of Copenhagen, Frederiksberg C, Denmark
| | - Gabriele Arcari
- Department of Molecular Medicine Sapienza, University of Rome, Rome, Italy
| | - Egle Kudirkiene
- Department of Veterinary and Animal Sciences, Section for Veterinary Clinical Microbiology, University of Copenhagen, Frederiksberg C, Denmark
| | - Riccardo Polani
- Department of Molecular Medicine Sapienza, University of Rome, Rome, Italy
| | | | - Peter Damborg
- Department of Veterinary and Animal Sciences, Section for Veterinary Clinical Microbiology, University of Copenhagen, Frederiksberg C, Denmark
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, Section for Veterinary Clinical Microbiology, University of Copenhagen, Frederiksberg C, Denmark
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Alotaibi K, Khan AA. Prevalence and Molecular Characterization of Shiga Toxin-Producing Escherichia coli from Food and Clinical Samples. Pathogens 2023; 12:1302. [PMID: 38003767 PMCID: PMC10675443 DOI: 10.3390/pathogens12111302] [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: 08/15/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is one of the most prominent food-borne pathogens in humans. The current study aims to detect and to analyze the virulence factors, antibiotic resistance, and plasmid profiles for forty-six STEC strains, isolated from clinical and food strains. Pulsed-field gel electrophoresis (PFGE) was used to determine the genetic relatedness between different serotypes and sources of samples. The clinical samples were found to be resistant to Nb (100%), Tet (100%), Amp (20%), SXT (15%), and Kan (15%) antibiotics. In contrast, the food strains were found to be resistant to Nb (100%), Tet (33%), Amp (16.6%), and SXT (16.6%) antibiotics. The PFGE typing of the forty-six isolates was grouped into more than ten clusters, each with a similarity between 30% and 70%. Most of the isolates were found positive for more than five virulence genes (eae, hlyA, stx1, stx2, stx2f, stx2c, stx2e, stx2, nelB, pagC, sen, toxB, irp, efa, and efa1). All the isolates carried different sizes of the plasmids. The isolates were analyzed for plasmid replicon type by PCR, and 72.5% of the clinical isolates were found to contain X replicon-type plasmid, 50% of the clinical isolates contained FIB replicon-type plasmid, and 17.5% of the clinical isolates contained Y replicon-type plasmid. Three clinical isolates contained both I1 and Hi1 replicon-type plasmid. Only two food isolates contained B/O and W replicon-type plasmid. These results indicate that STEC strains have diverse clonal populations among food and clinical strains that are resistant to several antimicrobials. In conclusion, our findings indicate that food isolates of STEC strains harbor virulence, antimicrobial resistance, plasmid replicon typing determinants like those of other STEC strains from clinical strains. These results suggest that these strains are unique and may contribute to the virulence of the isolates. Therefore, surveillance and characterization of STEC strains can provide useful information about the prevalence of STEC in food and clinical sources. Furthermore, it will help to identify STEC serotypes that are highly pathogenic to humans and may emerge as a threat to public health.
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Affiliation(s)
- Khulud Alotaibi
- Division of Microbiology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR 72079, USA;
- Department of Biology, University of Arkansas at Little Rock, Little Rock, AR 72205, USA
| | - Ashraf A. Khan
- Division of Microbiology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR 72079, USA;
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Rozwandowicz M, Kant A, Wagenaar J, Mevius D, Hordijk J, Brouwer M. Understanding the genetic basis of the incompatibility of IncK1 and IncK2 plasmids. OPEN RESEARCH EUROPE 2023; 3:53. [PMID: 38106640 PMCID: PMC10724649 DOI: 10.12688/openreseurope.15121.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/23/2023] [Indexed: 12/19/2023]
Abstract
Antimicrobial resistance is a persistent challenge in human and veterinary medicine, which is often encoded on plasmids which are transmissible between bacterial cells. Incompatibility is the inability of two plasmids to be stably maintained in one cell which is caused by the presence of identical or closely related shared determinants between two plasmids originating from partition or replication mechanisms. For I-complex plasmids in Enterobacteriacae, replication- based incompatibility is caused by the small antisense RNA stem-loop structure called RNAI. The I-complex plasmid group IncK consists of two compatible subgroups, IncK1 and IncK2, for which the RNAI differs only by five nucleotides. In this study we focussed on the interaction of the IncK1 and IncK2 RNAI structures by constructing minireplicons containing the replication region of IncK1 or IncK2 plasmids coupled with a kanamycin resistance marker. Using minireplicons excludes involvement of incompatibility mechanisms other than RNAI. Additionally, we performed single nucleotide mutagenesis targeting the five nucleotides that differ between the IncK1 and IncK2 RNAI sequences of these minireplicons. The obtained results show that a single nucleotide change in the RNAI structure is responsible for the compatible phenotype of IncK1 with IncK2 plasmids. Only nucleotides in the RNAI top loop and interior loop have an effect on minireplicon incompatibility with wild type plasmids, while mutations in the stem of the RNAI structure had no significant effect on incompatibility. Understanding the molecular basis of incompatibility is relevant for future in silico predictions of plasmid incompatibility.
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Affiliation(s)
- Marta Rozwandowicz
- National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Arie Kant
- Wageningen Bioveterinary Research, Lelystd, 8221 RA, The Netherlands
| | - Jaap Wagenaar
- Utrecht University, Utrecht, 3584 CS, The Netherlands
| | - Dik Mevius
- Wageningen Bioveterinary Research, Lelystd, 8221 RA, The Netherlands
| | - Joost Hordijk
- National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Michael Brouwer
- Wageningen Bioveterinary Research, Lelystd, 8221 RA, The Netherlands
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London LY, Lim CH, Modliszewski JL, Siddiqui NY, Sysoeva TA. Draft genomes of Lactobacillus delbrueckii and Klebsiella pneumoniae coexisting within a female urinary bladder. Microbiol Resour Announc 2023; 12:e0030523. [PMID: 37737617 PMCID: PMC10586092 DOI: 10.1128/mra.00305-23] [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: 04/14/2023] [Accepted: 07/30/2023] [Indexed: 09/23/2023] Open
Abstract
Here, we present the draft genome sequences of Lactobacillus delbrueckii and Klebsiella pneumoniae, both isolated from the urinary bladder of an asymptomatic post-menopausal female patient with a diagnosis of recurrent urinary tract infections. These genomes will facilitate analyses of interbacterial interactions in the urinary microbiome.
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Affiliation(s)
- Laricca Y. London
- Department of Biological and Environmental Sciences, Alabama A&M University, Normal, Alabama, USA
| | - Chae Hee Lim
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama, USA
| | - Jennifer L. Modliszewski
- Department of Bioinformatics and Biostatistics, Duke University Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Nazema Y. Siddiqui
- Department of Obstetrics and Gynecology, Division of Urogynecology and Reconstructive Pelvic Surgery, Duke University, Durham, North Carolina, USA
| | - Tatyana A. Sysoeva
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama, USA
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Uyanik T, Çadirci Ö, Gücükoğlu A, Bölükbaş A. Examining the presence of carbapenem resistant Enterobacterales and routes of transmission to bovine carcasses at slaughterhouses. Int J Food Microbiol 2023; 403:110314. [PMID: 37422948 DOI: 10.1016/j.ijfoodmicro.2023.110314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023]
Abstract
This study was conducted to investigate the existence and possible transmission routes of CREs during the bovine slaughter process. A total of 600 samples including rectoanal mucosal swaps, bovine hides and carcasses were collected weekly, over a 20 week period from three different slaughterhouses in Samsun province and analyzed in terms of CRE. Isolation of CRE was performed using Chromatic CRE Agar. Obtained isolates were identified using PCR and VITEK MS. E-test method was used for screening of carbapenemase production and disk diffusion method was used for detection of phenotypic carbapenem resistance. Presence of five major carbapenemase genes were investigated by PCR and obtained amplicons were sequenced by Sanger sequencing. Clonal relatedness was investigated by Clermont phylo-typing and MLST. Plasmid incompability groups were determined by PCR-based replicon typing. Based on the results, only one bovine hide sample was found positive in terms of CRE and blaKPC-2 harbouring E. coli ST398 (phylogroup A) was identified. E. coli ST398 was found resistant to meropenem, imipenem, ertapenem, doripenem and also tested fluoroquinolones. ST398 was found to harbour three distinct replicons, namely N, FIIK, and FIB KQ. Inc. groups for these replicons were identified as IncN and IncFIIK. On the other hand, no concrete evidence has been obtained to suggest that CREs are spreading at the slaughterhouse level. Conclusively, conducting further studies in areas such as farms, pens, and feedlots is necessary to gain a better understanding of the transmission routes of CREs in livestock.
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Affiliation(s)
- Tolga Uyanik
- Ondokuz Mayis University, Faculty of Veterinary Medicine, Department of Food Hygiene and Technology, Türkiye.
| | - Özgür Çadirci
- Ondokuz Mayis University, Faculty of Veterinary Medicine, Department of Food Hygiene and Technology, Türkiye
| | - Ali Gücükoğlu
- Ondokuz Mayis University, Faculty of Veterinary Medicine, Department of Food Hygiene and Technology, Türkiye
| | - Ayşegül Bölükbaş
- Ondokuz Mayis University, Faculty of Veterinary Medicine, Department of Food Hygiene and Technology, Türkiye
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Dwivedi A, Kumar CB, Kumar A, Soni M, Sahu V, Awasthi A, Rathore G. Detection of clinically relevant carbapenemase encoding genes in carbapenem-resistant Enterobacter cloacae complex and Klebsiella pneumoniae isolated from farmed freshwater fish. J Appl Microbiol 2023; 134:lxad212. [PMID: 37715332 DOI: 10.1093/jambio/lxad212] [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: 04/25/2023] [Revised: 08/30/2023] [Accepted: 09/14/2023] [Indexed: 09/17/2023]
Abstract
AIMS The present study was aimed to detect clinically relevant carbapenemase encoding genes in carbapenem-resistant Enterobacter cloacae complex (CR-ECC), Klebsiella pneumoniae (CR-KP), and Serratia plymuthica (CR-SP) isolated from farmed freshwater fish. METHODS AND RESULTS Out of 243 spatially diverse freshwater fish samples analysed, 5.3% were contaminated with CR-ECC, 1.6% with CR-KP, and 0.4% with CR-SP. The CR-ECC was further identified as E. asburiae (38.5%), E. mori (23.1%), E. cloacae (15.4%), E. hormaechei (15.4%), and E. kobei (7.7%) by 16S rRNA gene sequencing. The CR-ECC were resistant to carbapenems and cefoxitin, whereas CR-KP and CR-SP were multi-drug resistant (MDR). The CR-ECC harboured the carbapenemase gene blaIMI alone or in combination with blaTEM, blaEBC, blaCIT, blaACC, and tet(E). Whereas, CR-KP harboured carbapenemase gene, blaNDM-5 along with blaOXA-48, blaSHV, blaOXA-1, blaCTX-M-15, tet(A), sul1, and qnrB. No carbapenemase-encoding genes were detected in CR-SP. The MLST analysis showed that CR-KP belonged to ST231 and ST1561 lineages, while CR-ECC did not show exact match with any reported STs. The plasmid replicons predominantly detected were IncF and IncI1. Broth mating assays of CR-KP and CR-ECC with recipient Escherichia coli J53 indicated that blaNDM-5 was transferable but not blaIMI. CONCLUSION This study highlights the low-level contamination of carbapenem-resistant Enterobacterales (CRE) harbouring clinically relevant carbapenemase-encoding genes in farmed freshwater fish from India. The CR-ECC of fish origin did not show the potential to spread carbapenem resistance.
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Affiliation(s)
- Arti Dwivedi
- Exotics and Aquatic Animal Health (EAAH) Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226002, India
- Department of Biotechnology, Maharaja Agrasen University, Baddi, Solan 174103, India
| | - Chandra Bhushan Kumar
- Exotics and Aquatic Animal Health (EAAH) Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226002, India
| | - Anil Kumar
- Exotics and Aquatic Animal Health (EAAH) Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226002, India
| | - Mayank Soni
- Exotics and Aquatic Animal Health (EAAH) Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226002, India
| | - Vikash Sahu
- Exotics and Aquatic Animal Health (EAAH) Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226002, India
| | - Abhishek Awasthi
- Department of Biotechnology, Maharaja Agrasen University, Baddi, Solan 174103, India
| | - Gaurav Rathore
- Exotics and Aquatic Animal Health (EAAH) Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226002, India
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Tsai CH, Lee NY, Chao CM, Chen CC, Lai CC, Ho CH, Chen YC, Chen PY, Tang HJ, Chen HJ, Su BA, Lai HY, Chow JC, Chang TH. Emergence and dissemination of multidrug-resistant Escherichia coli ST8346 coharboring bla NDM-5 and bla OXA-181 in Southern Taiwan, 2017-2021. J Infect Public Health 2023; 16:1675-1681. [PMID: 37633229 DOI: 10.1016/j.jiph.2023.08.007] [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: 06/13/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/28/2023] Open
Abstract
BACKGROUND Enterobacterales carrying blaNDM represent an emerging challenge in treating infectious diseases. In this study, we aimed to investigate the characteristics of blaNDM-producing Enterobacterales from three hospitals in southern Taiwan. METHODS Enterobacterales strains that were nonsusceptible to more than one carbapenem (ertapenem, meropenem, imipenem, or doripenem) were collected from hospitalized patients. Molecular typing for New Delhi metallo-β-lactamase (NDM) and antibiotic susceptibility tests were performed, followed by multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and plasmid analysis by PCR-based replicon typing. RESULTS A total of 1311 carbapenem-nonsusceptible Enterobacterales were isolated from 2017 to 2021. blaNDM-encoding genes were detected in 108 isolates, with 53 (49.1%) harboring blaNDM-1 and 55 (50.9%) harboring blaNDM-5. The rate of blaNDM-1 detection among isolates decreased to 2% in 2021. However, the rate of E. coli harboring blaNDM-5 increased from 1% to 12% of total isolates during the study period. Of 47 NDM-5-positive E. coli isolates, 44 (93.6%) were ST8346 with high genetic relatedness. E. coli ST8346 isolates showed high-level resistance to both carbapenems and aminoglycosides. Most (38 out of 47, 80.9%) blaNDM-5-harboring E. coli isolates co-harbored blaOXA-181. We analyzed the regions harboring blaNDM-5 in E. coli ST8346 via PCR amplification. blaNDM-5 and blaOXA-181 were located on two separate plasmids, IncF and IncX3, respectively. CONCLUSION The dissemination of E. coli ST8346 caused an increase in blaNDM-5 and blaOXA-181 co-harboring Enterobacterales in southern Taiwan, which show high-level resistance to both carbapenems and aminoglycosides. We identified a distinct IncF plasmid encoding blaNDM-5 that has the potential for rapid spread and needs further surveillance.
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Affiliation(s)
- Chia-Hung Tsai
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Nan-Yao Lee
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Ming Chao
- Department of Intensive Care Medicine, Chi Mei Medical Center, Liouying, Tainan, Taiwan
| | - Chi-Chung Chen
- Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan; Department of Food Science, National Chiayi University, Chiayi, Taiwan
| | - Chih-Cheng Lai
- Division of Hospital Medicine, Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan; School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chung-Han Ho
- Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan; Department of Information Management, Southern Taiwan University of Science and Technology, Tainan, Taiwan
| | - Yu-Chin Chen
- Department of Pediatrics, Chi Mei Medical Center, Chiali, Tainan, Taiwan
| | - Po-Yu Chen
- Department of Nursing, Min-Hwei College of Health Care Management, Tainan, Taiwan
| | - Hung-Jen Tang
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Hung-Jui Chen
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Bo-An Su
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Hsin-Yu Lai
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Julie Chi Chow
- Department of Pediatrics, Chi Mei Medical Center, Tainan, Taiwan
| | - Tu-Hsuan Chang
- Department of Pediatrics, Chi Mei Medical Center, Tainan, Taiwan.
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Dey TK, Lindahl JF, Lundkvist Å, Grace D, Deka RP, Shome R, Bandyopadhyay S, Goyal NK, Sharma G, Shome BR. Analyses of Extended-Spectrum-β-Lactamase, Metallo-β-Lactamase, and AmpC-β-Lactamase Producing Enterobacteriaceae from the Dairy Value Chain in India. Antibiotics (Basel) 2023; 12:1449. [PMID: 37760745 PMCID: PMC10650101 DOI: 10.3390/antibiotics12091449] [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: 08/09/2023] [Revised: 09/03/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The consumption of milk contaminated with antibiotic-resistant bacteria poses a significant health threat to humans. This study aimed to investigate the prevalence of Enterobacteriaceae producing β-lactamases (ESBL, MBL, and AmpC) in cow and buffalo milk samples from two Indian states, Haryana and Assam. A total of 401 milk samples were collected from dairy farmers and vendors in the specified districts. Microbiological assays, antibiotic susceptibility testing, and PCR-based genotyping were employed to analyze 421 Gram-negative bacterial isolates. The overall prevalence of β-lactamase genes was 10% (confidence interval (CI) (7-13)), with higher rates in Haryana (13%, CI (9-19)) compared to Assam (7%, CI (4-11)). The identified β-lactamase genes in isolates were blaCMY, blaMOX, blaFOX, blaEBC, and blaDHA, associated with AmpC production. Additionally, blaCTX-M1, blaSHV, and blaTEM were detected as ESBL producers, while blaVIM, blaIMP, blaSPM, blaSIM, and blaGIM were identified as MBL producers. Notably, Shigella spp. were the dominant β-lactamase producers among identified Enterobacteriaceae. This study highlights the presence of various prevalent β-lactamase genes in milk isolates, indicating the potential risk of antimicrobial-resistant bacteria in dairy products. The presence of β-lactam resistance raises concern as this could restrict antibiotic options for treatment. The discordance between genotypic and phenotypic methods emphasizes the necessity for comprehensive approaches that integrate both techniques to accurately assess antibiotic resistance. Urgent collaborative action incorporating rational and regulated use of antibiotics across the dairy value chain is required to address the global challenge of β-lactam resistance.
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Affiliation(s)
- Tushar Kumar Dey
- Department of Biosciences, International Livestock Research Institute, Nairobi 00100, Kenya
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 75123 Uppsala, Sweden
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru 560064, India
| | - Johanna Frida Lindahl
- Department of Biosciences, International Livestock Research Institute, Nairobi 00100, Kenya
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 75123 Uppsala, Sweden
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 75123 Uppsala, Sweden
| | - Delia Grace
- Department of Biosciences, International Livestock Research Institute, Nairobi 00100, Kenya
- Food and Markets Department, Natural Resources Institute, Chatham Maritime ME4 4TB, UK
| | - Ram Pratim Deka
- International Livestock Research Institute, Regional Office for South Asia, New Delhi 110012, India
| | - Rajeswari Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru 560064, India
| | - Samiran Bandyopadhyay
- Eastern Regional Station, ICAR-Indian Veterinary Research Institute, Kolkata 700037, India
| | - Naresh Kumar Goyal
- Dairy Microbiology Division, National Dairy Research Institute, Karnal 132001, India
| | - Garima Sharma
- Department of Biosciences, International Livestock Research Institute, Nairobi 00100, Kenya
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 75123 Uppsala, Sweden
| | - Bibek Ranjan Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru 560064, India
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Abdelbary ER, Elsaghier AM, Abd El-Baky RM, Waly NGFM, Ramadan M, Abd- Elsamea FS, Ali ME, Alzahrani HA, Salah M. First Emergence of NDM-5 and OqxAB Efflux Pumps Among Multidrug-Resistant Klebsiella pneumoniae Isolated from Pediatric Patients in Assiut, Egypt. Infect Drug Resist 2023; 16:5965-5976. [PMID: 37705515 PMCID: PMC10496925 DOI: 10.2147/idr.s421978] [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: 06/01/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023] Open
Abstract
Introduction New Delhi metallo-β-lactamase (NDM)-producing K. pneumoniae poses a high risk, especially among Egyptian pediatric patients who consume carbapenems antibiotics very widely and without adequate diagnostic sources. In addition, presence of efflux pump genes such as OqxAB increases resistance against many groups of antimicrobials which exacerbates the problem faced for human health. This study aimed to determine NDM variants among K. pneumoniae strains isolated from pediatric patients in Egypt, analyze the presence of OqxAB genes, and molecular characterization of blaNDM-5-positive K. pneumoniae. Methods Fifty-six K. pneumoniae isolates were recovered from pediatric patients, and tested for carbapenemase by modified carbapenem inactivation methods (mCIM) test. Minimum inhibitory concentrations of meropenem and colistin were determined by meropenem E-test strips and broth microdilution, respectively. PCR was used for the detection of the resistant genes (ESBL gene (blaCTX-M), carbapenemase genes (blaNDM, blaKPC) colistin resistant (mcr1, mcr2)) and genes for efflux pump (oqxA and oqxB). BlaNDM was sequenced. The effect of efflux pump in NDM-5-producing isolates was assessed by measuring MIC of ciprofloxacin and meropenem before and after exposure to the carbonyl cyanide 3-chlorophenylhydrazone (CCCP). The horizontal gene transfer ability of blaNDM-5 was determined using liquid mating assay and PCR-based replicon typing (PBRT) was done to determine the major plasmid incompatibility group. Results Twenty-nine isolates were positive for blaNDM-1, nine isolates were positive for blaNDM-5, and 15 isolates were positive for blaKPC. There is a significant increase of meropenem MIC of NDM-5-positive isolates compared with NDM-1-positive isolates. In addition, 38 isolates were positive for CTX-M, and 15 isolates were positive for mcr1. Both OqxA and OqxB were detected in 26 isolates and 13 isolates were positive for OqxA while 11 isolates were positive for OqxB only. All NDM-5-producing isolates except one isolate could transfer their plasmids by conjugation to their corresponding transconjugants (E. coli J53). Plasmid replicon typing showed that FII was predominant in NDM-5-producing K. pneumoniae. Similar strains were found between the three isolates and similarity was also detected between the two isolates. Conclusion The highly resistant K. pneumoniae producing blaNDM-5 type was firstly isolated from pediatric patients. The association of efflux pump genes such as OqxAB is involved in resistance to ciprofloxacin. This highlighted the severity risk of blaNDM-5-positive K. pneumonia as it could transfer blaNDM-5 to other bacteria and has more resistance against carbapenems. This underlines the importance of continuous monitoring of infection control guidelines, and the urgent need for a national antimicrobial stewardship plan in Egyptian hospitals.
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Affiliation(s)
- Eman R Abdelbary
- Microbiology and Immunology Department, Faculty of Pharmacy, Al-Azhar University-Assiut Branch, Assiut, 11651, Egypt
| | - Ashraf M Elsaghier
- Gastroenterology and Hepatology Unit, University Children Hospital, Faculty of Medicine, Assiut University, Assiut, 11651, Egypt
| | - Rehab M Abd El-Baky
- Microbiology and Immunology Department, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
- Microbiology and Immunology Department, Faculty of Pharmacy, Deraya University, Minia, 11566, Egypt
| | - Nancy G F M Waly
- Microbiology and Immunology Department, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Mohammed Ramadan
- Microbiology and Immunology Department, Faculty of Pharmacy, Al-Azhar University-Assiut Branch, Assiut, 11651, Egypt
| | - Fatma S Abd- Elsamea
- Medical Microbiology and Immunology Department, Faculty of Medicine, Assiut University, Assiut, 11651, Egypt
| | - Mohamed E Ali
- Microbiology and Immunology Department, Faculty of Pharmacy, Al-Azhar University-Assiut Branch, Assiut, 11651, Egypt
| | - Hayat A Alzahrani
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, Northern Border University, Arar, 91431, Saudi Arabia
| | - Mohammed Salah
- Microbiology and Immunology Department, Faculty of Pharmacy, Port Said University, Port Said City, 42526, Egypt
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Martínez-Álvarez S, Châtre P, Cardona-Cabrera T, François P, Sánchez-Cano A, Höfle U, Zarazaga M, Madec JY, Haenni M, Torres C. Detection and genetic characterization of bla ESBL-carrying plasmids of cloacal Escherichia coli isolates from white stork nestlings (Ciconia ciconia) in Spain. J Glob Antimicrob Resist 2023; 34:186-194. [PMID: 37482121 DOI: 10.1016/j.jgar.2023.07.011] [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: 05/10/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023] Open
Abstract
OBJECTIVES This study aimed to characterize Escherichia coli isolates from cloacal samples of white stork nestlings, with a special focus on extended-spectrum β-lactamases (ESBLs)-producing E. coli isolates and their plasmid content. METHODS Cloacal samples of 88 animals were seeded on MacConkey-agar and chromogenic-ESBL plates to recover E. coli and ESBL-producing E. coli. Antimicrobial susceptibility was screened using the disc diffusion method, and the genotypic characterization was performed by polymerase chain reaction (PCR) and subsequent sequencing. S1 nuclease Pulsed-Field-Gel-Electrophoresis (PFGE), Southern blotting, and conjugation essays were performed on ESBL-producing E. coli, as well as whole-genome sequencing by short- and long-reads. The four blaESBL-carrying plasmids were completely sequenced. RESULTS A total of 113 non-ESBL-producing E. coli isolates were collected on antibiotic-free MacConkey-agar, of which 27 (23.9%) showed a multidrug-resistance (MDR) phenotype, mainly associated with β-lactam-phenicol-sulfonamide resistance (blaTEM/cmlA/floR/sul1/sul2/sul3). Moreover, four white stork nestlings carried ESBL-producing E. coli (4.5%) with the following characteristics: blaSHV-12/ST38-D, blaSHV-12/ST58-B1, blaCTX-M-1/ST162-B1, and blaCTX-M-32/ST155-B1. Whole-genome sequencing followed by Southern blot hybridizations on S1-PFGE gels in ESBL-positive isolates proved that the blaCTX-M-1 gene and one of the blaSHV-12 genes were carried by IncI1/pST3 plasmids, while the second blaSHV-12 gene and the blaCTX-M-32 gene were located on IncF plasmids. The two blaSHV-12 genes and the two blaCTX-M genes had similar but non-identical close genetic environments, as all four genes were flanked by a variety of insertion sequences. CONCLUSION The role played by several genetic platforms in the mobility of ESBL genes allows for interchangeability on a remarkably small scale (gene-plasmid-clones), which may support the spread of ESBL genes.
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Affiliation(s)
- Sandra Martínez-Álvarez
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Pierre Châtre
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Teresa Cardona-Cabrera
- Health and Biotechnology (SaBio) Research Group, Institute for Game and Wildlife Research IREC (CSIC-UCLM), Ciudad Real, Spain
| | - Pauline François
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Alberto Sánchez-Cano
- Health and Biotechnology (SaBio) Research Group, Institute for Game and Wildlife Research IREC (CSIC-UCLM), Ciudad Real, Spain
| | - Ursula Höfle
- Health and Biotechnology (SaBio) Research Group, Institute for Game and Wildlife Research IREC (CSIC-UCLM), Ciudad Real, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain.
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Arredondo-Alonso S, Gladstone R, Pöntinen A, Gama J, Schürch A, Lanza V, Johnsen P, Samuelsen Ø, Tonkin-Hill G, Corander J. Mge-cluster: a reference-free approach for typing bacterial plasmids. NAR Genom Bioinform 2023; 5:lqad066. [PMID: 37435357 PMCID: PMC10331934 DOI: 10.1093/nargab/lqad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/08/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
Extrachromosomal elements of bacterial cells such as plasmids are notorious for their importance in evolution and adaptation to changing ecology. However, high-resolution population-wide analysis of plasmids has only become accessible recently with the advent of scalable long-read sequencing technology. Current typing methods for the classification of plasmids remain limited in their scope which motivated us to develop a computationally efficient approach to simultaneously recognize novel types and classify plasmids into previously identified groups. Here, we introduce mge-cluster that can easily handle thousands of input sequences which are compressed using a unitig representation in a de Bruijn graph. Our approach offers a faster runtime than existing algorithms, with moderate memory usage, and enables an intuitive visualization, classification and clustering scheme that users can explore interactively within a single framework. Mge-cluster platform for plasmid analysis can be easily distributed and replicated, enabling a consistent labelling of plasmids across past, present, and future sequence collections. We underscore the advantages of our approach by analysing a population-wide plasmid data set obtained from the opportunistic pathogen Escherichia coli, studying the prevalence of the colistin resistance gene mcr-1.1 within the plasmid population, and describing an instance of resistance plasmid transmission within a hospital environment.
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Affiliation(s)
| | | | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - João A Gama
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anita C Schürch
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Val F Lanza
- CIBERINFEC, Madrid, Spain
- Bioinformatics Unit, University Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
| | - Pål Jarle Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Gerry Tonkin-Hill
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, Helsinki, Finland
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