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Nasser F, Gaudreau A, Lubega S, Zaker A, Xia X, Mer AS, D'Costa VM. Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter. Emerg Microbes Infect 2024; 13:2320929. [PMID: 38530969 DOI: 10.1080/22221751.2024.2320929] [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: 09/14/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.
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Affiliation(s)
- Farah Nasser
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Avery Gaudreau
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Shareefah Lubega
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Arvin Zaker
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Xuhua Xia
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
- Department of Biology, University of Ottawa, Ottawa, Canada
| | - Arvind S Mer
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Vanessa M D'Costa
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
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Verburg I, Hernández Leal L, Waar K, Rossen JWA, Schmitt H, García-Cobos S. Klebsiella pneumoniae species complex: From wastewater to the environment. One Health 2024; 19:100880. [PMID: 39263320 PMCID: PMC11387367 DOI: 10.1016/j.onehlt.2024.100880] [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: 05/08/2024] [Revised: 08/15/2024] [Accepted: 08/15/2024] [Indexed: 09/13/2024] Open
Abstract
Klebsiella pneumoniae plays a significant role in nosocomial infections and spreading antibiotic resistance, and therefore forms a major threat to public health. In this study, we investigated the role of the wastewater pathway in the spread of pathogenic bacteria and more specifically, in the spread of antibiotic resistant Klebsiella pneumoniae subspecies. Whole-genome sequencing was performed of 185 K. pneumoniae isolates collected from hospital, nursing home, and community wastewater, the receiving wastewater treatment plant (WWTP), and clinical isolates from the investigated hospital. K. pneumoniae isolates from different sources were not genetically related, except for WWTP influent (46.5%) and effluent (62.5%), revealing survival of bacteria from wastewater treatment. The content of antibiotic resistance (ARGs), virulence, and plasmid replicon genes differed between K. pneumoniae subspecies and their origin. While chromosomal bla genes were specific for each K. pneumoniae subspecies, bla genes predicted in plasmid contigs were found in several K. pneumoniae subspecies, implying possible gene transfer between subspecies. Transferable ARGs were most abundant in patients and hospital isolates (70%), but the average number of plasmid replicon genes per isolate was similar across all sources, showing plasmid content being more relevant than plasmid quantity. Most patient (90%) and hospital wastewater (34%) isolates were K. pneumoniae subsp. pneumoniae, and the yersiniabactin cluster genes ybt, fyuA, and irp12 were only found in this subspecies, as were the IncFII(pECLA), IncHI2A, and IncHI2 plasmid replicon genes, suggesting the clinical origin of these type of plasmids.
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Affiliation(s)
- Ilse Verburg
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900, CC, Leeuwarden, the Netherlands
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713, GZ, Groningen, the Netherlands
| | - Lucia Hernández Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900, CC, Leeuwarden, the Netherlands
| | - Karola Waar
- Certe Medische Microbiologie Friesland, 8900, JA, Leeuwarden, the Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713, GZ, Groningen, the Netherlands
| | - Heike Schmitt
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900, CC, Leeuwarden, the Netherlands
- Institute for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721, MA, Bilthoven, the Netherlands
| | - Silvia García-Cobos
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713, GZ, Groningen, the Netherlands
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
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Sattler J, Noster J, Stelzer Y, Spille M, Schäfer S, Xanthopoulou K, Sommer J, Jantsch J, Peter S, Göttig S, Gatermann SG, Hamprecht A. OXA-48-like carbapenemases in Proteus mirabilis - novel genetic environments and a challenge for detection. Emerg Microbes Infect 2024; 13:2353310. [PMID: 38712879 PMCID: PMC11123474 DOI: 10.1080/22221751.2024.2353310] [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: 01/01/2024] [Accepted: 05/05/2024] [Indexed: 05/08/2024]
Abstract
OXA-48-like enzymes represent the most frequently detected carbapenemases in Enterobacterales in Western Europe, North Africa and the Middle East. In contrast to other species, the presence of OXA-48-like in Proteus mirabilis leads to an unusually susceptible phenotype with low MICs for carbapenems and piperacillin-tazobactam, which is easily missed in the diagnostic laboratory. So far, there is little data available on the genetic environments of the corresponding genes, blaOXA-48-like, in P. mirabilis. In this study susceptibility phenotypes and genomic data of 13 OXA-48-like-producing P. mirabilis were investigated (OXA-48, n = 9; OXA-181, n = 3; OXA-162, n = 1). Ten isolates were susceptible to meropenem and ertapenem and three isolates were susceptible to piperacillin-tazobactam. The gene blaOXA-48 was chromosomally located in 7/9 isolates. Thereof, in three isolates blaOXA-48 was inserted into a P. mirabilis genomic island. Of the three isolates harbouring blaOXA-181 one was located on an IncX3 plasmid and two were located on a novel MOBF plasmid, pOXA-P12, within the new transposon Tn7713. In 5/6 isolates with plasmidic location of blaOXA-48-like, the plasmids could conjugate to E. coli recipients in vitro. Vice versa, blaOXA-48-carrying plasmids could conjugate from other Enterobacterales into a P. mirabilis recipient. These data show a high diversity of blaOXA-48-like genetic environments compared to other Enterobacterales, where genetic environments are quite homogenous. Given the difficult-to-detect phenotype of OXA-48-like-producing P. mirabilis and the location of blaOXA-48-like on mobile genetic elements, it is likely that OXA-48-like-producing P. mirabilis can disseminate, escape most surveillance systems, and contribute to a hidden spread of OXA-48-like.
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Affiliation(s)
- Janko Sattler
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
- German Centre for Infection Research (DZIF)
| | - Janina Noster
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
| | - Yvonne Stelzer
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
| | - Martina Spille
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
| | - Sina Schäfer
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF)
| | - Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF)
| | - Julian Sommer
- Goethe University Frankfurt, University Hospital, Institute of Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Jonathan Jantsch
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF)
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University Hospital Tuebingen, Tuebingen, Germany
- German Centre for Infection Research (DZIF)
| | - Stephan Göttig
- Goethe University Frankfurt, University Hospital, Institute of Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Sören G. Gatermann
- National Reference Laboratory for Multidrug-Resistant Gram-negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
- German Centre for Infection Research (DZIF)
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Siderius NL, Sapula SA, Hart BJ, Hutchings JL, Venter H. Enterobacter adelaidei sp. nov. Isolation of an extensively drug resistant strain from hospital wastewater in Australia and the global distribution of the species. Microbiol Res 2024; 288:127867. [PMID: 39163716 DOI: 10.1016/j.micres.2024.127867] [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: 05/16/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 08/22/2024]
Abstract
BACKGROUND Enterobacter species are included among the normal human gut microflora and persist in a diverse range of other environmental niches. They have become important opportunistic nosocomial pathogens known to harbour plasmid-mediated multi-class antimicrobial resistance (AMR) determinants. Global AMR surveillance of Enterobacterales isolates shows the genus is second to Klebsiella in terms of frequency of carbapenem resistance. Enterobacter taxonomy is confusing and standard species identification methods are largely inaccurate or insufficient. There are currently 27 named species and a total of 46 taxa in the genus distinguishable via average nucleotide identity (ANI) calculation between pairs of genomic sequences. Here we describe an Enterobacter strain, ECC3473, isolated from the wastewater of an Australian hospital whose species could not be determined by standard methods nor by ribosomal RNA gene multi-locus typing. AIM To characterise ECC3473 in terms of phenotypic and genotypic antimicrobial resistance, biochemical characteristics and taxonomy as well as to determine the global distribution of the novel species to which it belongs. METHODS Standard broth dilution and disk diffusion were used to determine phenotypic AMR. The strain's complete genome, including plasmids, was obtained following long- and short read sequencing and a novel long/short read hybrid assembly and polishing, and the genomic basis of AMR was determined. Phylogenomic analysis and quantitative measures of relatedness (ANI, digital DNA-DNA hybridisation, and difference in G+C content) were used to study the taxonomic relationship between ECC3473 and Enterobacter type-strains. NCBI and PubMLST databases and the literature were searched for additional members of the novel species to determine its global distribution. RESULTS ECC3473 is one of 21 strains isolated globally belonging to a novel Enterobacter species for which the name, Enterobacter adelaidei sp. nov. is proposed. The novel species was found to be resilient in its capacity to persist in contaminated water and adaptable in its ability to accumulate multiple transmissible AMR determinants. CONCLUSION E. adelaidei sp. nov. may become increasingly important to the dissemination of AMR.
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Affiliation(s)
- Naomi L Siderius
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Sylvia A Sapula
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Bradley J Hart
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Joshua L Hutchings
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Henrietta Venter
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
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Bertrans-Tubau L, Martínez-Campos S, Lopez-Doval J, Abril M, Ponsá S, Salvadó V, Hidalgo M, Pico-Tomàs A, Balcazar JL, Proia L. Nature-based bioreactors: Tackling antibiotic resistance in urban wastewater treatment. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 22:100445. [PMID: 39055482 PMCID: PMC11269294 DOI: 10.1016/j.ese.2024.100445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
The overuse and misuse of antibiotics have accelerated the selection of antibiotic-resistant bacteria, significantly impacting human, animal, and environmental health. As aquatic environments are vulnerable to antibiotic resistance, suitable management practices should be adopted to tackle this phenomenon. Here we show an effective, nature-based solution for reducing antibiotic resistance from actual wastewater. We utilize a bioreactor that relies on benthic (biofilms) and planktonic microbial communities to treat secondary effluent from a small urban wastewater treatment plant (<10,000 population equivalent). This treated effluent is eventually released into the local aquatic ecosystem. We observe high removal efficiency for genes that provide resistance to commonly used antibiotic families, as well as for mobile genetic elements that could potentially aid in their spread. Importantly, we notice a buildup of sulfonamide (sul1 and sul2) and tetracycline (tet(C), tet(G), and tetR) resistance genes specifically in biofilms. This advancement marks the initial step in considering this bioreactor as a nature-based, cost-effective tertiary treatment option for small UWWTPs facing antibiotic resistance challenges.
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Affiliation(s)
- Lluís Bertrans-Tubau
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Sergio Martínez-Campos
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Julio Lopez-Doval
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Meritxell Abril
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Sergio Ponsá
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Victoria Salvadó
- Chemistry Department, University of Girona. Campus Montilivi, 17005, Girona, Spain
| | - Manuela Hidalgo
- Chemistry Department, University of Girona. Campus Montilivi, 17005, Girona, Spain
| | - Anna Pico-Tomàs
- Catalan Institute Water Research (ICRA-CERCA), Emili Grahit 101, 17003, Girona, Spain
| | - Jose Luis Balcazar
- Catalan Institute Water Research (ICRA-CERCA), Emili Grahit 101, 17003, Girona, Spain
- University of Girona, 17004, Girona, Spain
| | - Lorenzo Proia
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
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de Paula Nogueira Cruz F, Marques de Andrade PH, Paiva de Sousa C, Teixeira Lacava P. Draft genome sequence of Bacillus velezensis endophytically isolated from roots of Polygala paniculata. Microbiol Resour Announc 2024; 13:e0082624. [PMID: 39283091 PMCID: PMC11465904 DOI: 10.1128/mra.00826-24] [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: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 10/11/2024] Open
Abstract
Polygala paniculata is a medicinal plant that harbors a remaining unknown microbiome. Those plants are known for their analgesic and anti-inflammatory properties and are widely found in the Brazilian Atlantic Forest. Herein, we report the isolation of the endophyte Bacillus velezensis GPP30 with a draft genome estimated at 4.0 Mpb.
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Affiliation(s)
- Felipe de Paula Nogueira Cruz
- Natural and Physical Sciences Department, Graceland University, Lamoni, Iowa, USA
- Laboratory of Microbiology and Biomolecules—LaMiB, Department of Morphology and Pathology, Federal University of São Carlos, São Carlos, São Paulo, Brazil
- Biotechnology Post Graduate Program, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | - Paulo Henrique Marques de Andrade
- Laboratory of Microbiology and Biomolecules—LaMiB, Department of Morphology and Pathology, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | - Cristina Paiva de Sousa
- Laboratory of Microbiology and Biomolecules—LaMiB, Department of Morphology and Pathology, Federal University of São Carlos, São Carlos, São Paulo, Brazil
- Biotechnology Post Graduate Program, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | - Paulo Teixeira Lacava
- Laboratory of Microbiology and Biomolecules—LaMiB, Department of Morphology and Pathology, Federal University of São Carlos, São Carlos, São Paulo, Brazil
- Biotechnology Post Graduate Program, Federal University of São Carlos, São Carlos, São Paulo, Brazil
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He X, Tang J, He S, Huang X. Analysis of risk factors and different treatments for infections caused by carbapenem-resistant Acinetobacter baumannii in Shaanxi, China. BMC Infect Dis 2024; 24:1130. [PMID: 39385067 PMCID: PMC11465493 DOI: 10.1186/s12879-024-10036-5] [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: 01/15/2024] [Accepted: 10/01/2024] [Indexed: 10/11/2024] Open
Abstract
BACKGROUND The global threat of Carbapenem-resistant Acinetobacter baumannii (CRAB) has intensified as resistance to carbapenems continues to rise in recent decades. We aimed to explore risk factors, molecular epidemiology, and antimicrobial therapy of CRAB infection. METHODS The clinical data of 110 patients infected with A. baumannii from December 2021 to December 2022 were retrospectively analyzed. Patients were divided into a carbapenem-resistance group (55 patients) and carbapenem-sensitive group (CSAB; 55 patients) based on resistance to carbapenem, and the risk factors of patients infected with CRAB were analyzed. Fifty-five patients with CRAB infection who received antimicrobial therapy were divided into a combination therapy group (45 patients) and a monotherapy group (10 patients), and differences between the two groups were compared. Whole-genome sequencing analysis was performed to assess resistance genes. Phylogenetic analysis was performed to explore the characteristics of CRAB isolates. RESULTS Among the total 110 patients, the rate of poor prognosis in the CRAB group was 43.6% (24/55). Mechanical ventilation (odds ratio [OR] = 5.364, 95% confidence interval [CI] 1.462-19.679, P = 0.011) and puncture (OR = 19.935, 95% CI 1.261-315.031, P = 0.012) were independent risk factors for CRAB infection. Of 55 patients in the antimicrobial regimen study, 45 received combination therapy (including dual, triple, or quadruple antibiotic therapy) and 10 received monotherapy. Univariate analysis revealed significant differences between the combination group and monotherapy group for admission to the intensive care unit and wound infection (P < 0.05). The CRAB strains of 26 patients taking carbapenem-based combination therapy were mainly ST208, ST1968, and ST195, among which patients with ST1968 strains had higher 28-day mortality. Furthermore, the blaOXA-23 gene was harbored in ST1968, ST195, and ST208. CONCLUSIONS Mortality was significantly higher in patients infected with CRAB than with CSAB. Mechanical ventilation and puncture were independent risk factors in predicting CRAB infections. The distribution of CRAB was dominated by ST208, ST1968, and ST195, among which patients with ST1968 had higher 28-day mortality. The blaOXA-23 gene appears to be widely disseminated.
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Affiliation(s)
- Xiaoliang He
- Department of Clinical Laboratory, Hanzhong Central Hospital, 22 Kangfu Road, Hanzhong, Shaanxi, People's Republic of China
| | - Jin Tang
- Department of Clinical Laboratory, Hanzhong Central Hospital, 22 Kangfu Road, Hanzhong, Shaanxi, People's Republic of China
| | - Sanjun He
- Department of Clinical Laboratory, Hanzhong Central Hospital, 22 Kangfu Road, Hanzhong, Shaanxi, People's Republic of China
| | - Xiaoxia Huang
- Department of Clinical Laboratory, Hanzhong Central Hospital, 22 Kangfu Road, Hanzhong, Shaanxi, People's Republic of China.
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Marin J, Walewski V, Braun T, Dziri S, Magnan M, Denamur E, Carbonnelle E, Bridier-Nahmias A. Genomic evidence of Escherichia coli gut population diversity translocation in leukemia patients. mSphere 2024:e0053024. [PMID: 39365076 DOI: 10.1128/msphere.00530-24] [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: 06/24/2024] [Accepted: 09/09/2024] [Indexed: 10/05/2024] Open
Abstract
Escherichia coli, a commensal species of the human gut, is an opportunistic pathogen that can reach extra-intestinal compartments, including the bloodstream and the bladder, among others. In non-immunosuppressed patients, purifying or neutral evolution of E. coli populations has been reported in the gut. Conversely, it has been suggested that when migrating to extra-intestinal compartments, E. coli genomes undergo diversifying selection as supported by strong evidence for adaptation. The level of genomic polymorphism and the size of the populations translocating from gut to extra-intestinal compartments is largely unknown. To gain insights into the pathophysiology of these translocations, we investigated the level of polymorphism and the evolutionary forces acting on the genomes of 77 E. coli isolated from various compartments in three immunosuppressed patients. Each patient had a unique strain, which was a mutator in one case. In all instances, we observed that translocation encompasses much of the genomic diversity present in the gut. The same signature of selection, whether purifying or diversifying, and as anticipated, neutral for mutator isolates, was observed in both the gut and bloodstream. Additionally, we found a limited number of non-specific mutations among compartments for non-mutator isolates. In all cases, urine isolates were dominated by neutral selection. These findings indicate that substantial proportions of populations are undergoing translocation and that they present a complex compartment-specific pattern of selection at the patient level.IMPORTANCEIt has been suggested that intra and extra-intestinal compartments differentially constrain the evolution of E. coli strains. Whether host particular conditions, such as immunosuppression, could affect the strain evolutionary trajectories remains understudied. We found that, in immunosuppressed patients, large fractions of E. coli gut populations are translocating with variable modifications of the signature of selection for commensal and pathogenic isolates according to the compartment and/or the patient. Such multiple site sampling should be performed in large cohorts of patients to gain a better understanding of E. coli extra-intestinal diseases.
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Affiliation(s)
- Julie Marin
- Université Sorbonne Paris Nord, INSERM, IAME, Bobigny, France
| | - Violaine Walewski
- APHP, HUPSSD, Hôpital Avicenne, Service de Microbiologie clinique, Bobigny, France
| | - Thorsten Braun
- Université Sorbonne Paris Nord, INSERM, IAME, Bobigny, France
- APHP, HUPSSD, Hôpital Avicenne, Service de Microbiologie clinique, Bobigny, France
| | - Samira Dziri
- APHP, HUPSSD, Hôpital Avicenne, Service de Microbiologie clinique, Bobigny, France
| | - Mélanie Magnan
- Université Paris Cité, INSERM, IAME, and APHP, Hôpital Bichat, Laboratoire de Génétique Moléculaire, Paris, France
| | - Erick Denamur
- Université Paris Cité, INSERM, IAME, and APHP, Hôpital Bichat, Laboratoire de Génétique Moléculaire, Paris, France
| | - Etienne Carbonnelle
- Université Sorbonne Paris Nord, INSERM, IAME, Bobigny, France
- APHP, HUPSSD, Hôpital Avicenne, Service de Microbiologie clinique, Bobigny, France
| | - Antoine Bridier-Nahmias
- Université Paris Cité, INSERM, IAME, and APHP, Hôpital Bichat, Laboratoire de Génétique Moléculaire, Paris, France
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Swinkels AF, Fischer EAJ, Korving L, Kusters NE, Wagenaar JA, Zomer AL. Selection for amoxicillin-, doxycycline-, and enrofloxacin-resistant Escherichia coli at concentrations lower than the ECOFF in broiler-derived cecal fermentations. Microbiol Spectr 2024; 12:e0097024. [PMID: 39269186 PMCID: PMC11448166 DOI: 10.1128/spectrum.00970-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024] Open
Abstract
Antimicrobial resistance (AMR) is an emerging worldwide problem and a health threat for humans and animals. Antimicrobial usage in human and animal medicine or in agriculture results in selection for AMR. The selective concentration of antimicrobial compounds can be lower than the minimum inhibitory concentration and differs between environments, which can be a reason for bacterial resistance. Therefore, knowledge of the minimal selective concentration (MSC), under natural conditions, is essential to understand the selective window of bacteria when exposed to residual antimicrobials. In this study, we estimated the MSCs of three antimicrobials, amoxicillin, doxycycline, and enrofloxacin in a complex microbial community by conducting fermentation assays with cecal material derived from broilers. We examined the phenotypic resistance of Escherichia coli, resistome, and microbiome after 6 and 30 hours of fermenting in the presence of the antimicrobials of interest. The concentrations were estimated to be 10-100 times lower than the epidemiological cut-off values in E. coli for the respective antimicrobials as determined by EUCAST, resulting in an MSC between 0.08 and 0.8 mg/L for amoxicillin, 0.4 and 4 mg/L for doxycycline, and 0.0125 and 0.125 mg/L for enrofloxacin. Additionally, resistome analysis provided an MSC for doxycycline between 0.4 and 4 mg/L, but amoxicillin and enrofloxacin exposure did not induce a significant difference. Our findings indicate at which concentrations there is still selection for antimicrobial-resistant bacteria. This knowledge can be used to manage the risk of the emergence of antimicrobial-resistant bacteria.IMPORTANCEAntimicrobial resistance possibly affects human and animal health, as well as economic prosperity in the future. The rise of antimicrobial-resistant bacteria is a consequence of using antimicrobial compounds in humans and animals selecting for antimicrobial-resistant bacteria. Concentrations reached during treatment are known to be selective for resistant bacteria. However, at which concentrations residues are still selective is important, especially for antimicrobial compounds that remain in the environment at low concentrations. The data in this paper might inform decisions regarding guidelines and regulations for the use of specific antimicrobials. In this study, we are providing these minimal selective concentrations for amoxicillin, doxycycline, and enrofloxacin in complex environments.
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Affiliation(s)
- Aram F. Swinkels
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Egil A. J. Fischer
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Lisa Korving
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Nina E. Kusters
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jaap A. Wagenaar
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Wageningen Bioveterinary Research, Lelystad, the Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Aldert L. Zomer
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
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10
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Ma Z, Qian C, Yao Z, Tang M, Chen K, Zhao D, Hu P, Zhou T, Cao J. Coexistence of plasmid-mediated tmexCD2-toprJ2, blaIMP-4, and blaNDM-1 in Klebsiella quasipneumoniae. Microbiol Spectr 2024; 12:e0387423. [PMID: 39162556 PMCID: PMC11448383 DOI: 10.1128/spectrum.03874-23] [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: 11/15/2023] [Accepted: 07/07/2024] [Indexed: 08/21/2024] Open
Abstract
Klebsiella quasipneumoniae is a potential pathogen that has not been studied comprehensively. The emergence of multidrug-resistant (MDR) K. quasipneumoniae, specifically strains resistant to tigecycline and carbapenem, presents a significant challenge to clinical treatment. This investigation aimed to characterize MDR K. quasipneumoniae strain FK8966, co-carrying tmexCD2-toprJ2, blaIMP-4, and blaNDM-1 by plasmids. It was observed that FK8966's MDR was primarily because of the IncHI1B-like plasmid co-carrying tmexCD2-toprJ2 and blaIMP-4, and an IncFIB(K)/IncFII(K) plasmid harboring blaNDM-1. Furthermore, the phylogenetic analysis revealed that IncHI1B-like plasmids carrying tmexCD2-toprJ2 were disseminated among different bacteria, specifically in China. Additionally, according to the comparative genomic analysis, the MDR regions indicated that the tmexCD2-toprJ2 gene cluster was inserted into the umuC gene, while blaIMP-4 was present in transposon TnAs3 linked to the class 1 integron (IntI1). It was also observed that an ΔTn3000 insertion with blaNDM-1 made a novel blaNDM-1 harboring IncFIB(K)/IncFII(K) plasmid. The antimicrobial resistance prevalence and phylogenetic analyses of K. quasipneumoniae strains indicated that FK8966 is a distinct MDR branch of K. quasipneumoniae. Furthermore, CRISPR-Cas system analysis showed that many K. quasipneumoniae CRISPR-Cas systems lacked spacers matching the two aforementioned novel resistance plasmids, suggesting that these resistance plasmids have the potential to disseminate within K. quasipneumoniae. Therefore, the spread of MDR K. quasipneumoniae and plasmids warrants further attention.IMPORTANCEThe emergence of multidrug-resistant K. quasipneumoniae poses a great threat to clinical care, and the situation is exacerbated by the dissemination of tigecycline- and carbapenem-resistant genes. Therefore, monitoring these pathogens and their resistance plasmids is urgent and crucial. This study identified tigecycline- and carbapenem-resistant K. quasipneumoniae strain, FK8966. Furthermore, it is the first study to report the coexistence of tmexCD2-toprJ2, blaIMP-4, and blaNDM-1 in K. quasipneumoniae. Moreover, the CRISPR-Cas system of many K. quasipneumoniae lacks spacers that match the plasmids carried by FK8966, which are crucial for mediating resistance against tigecycline and carbapenems, indicating their potential to disseminate within K. quasipneumoniae.
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Affiliation(s)
- Zhexiao Ma
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Changrui Qian
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Zhuocheng Yao
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Miran Tang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Kaixin Chen
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Deyi Zhao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Panjie Hu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Tieli Zhou
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jianming Cao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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11
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Fernández-Palacios P, Galán-Sánchez F, Casimiro-Soriguer CS, Jurado-Tarifa E, Arroyo F, Lara M, Chaves JA, Dopazo J, Rodríguez-Iglesias MA. Genotypic characterization and antimicrobial susceptibility of human Campylobacter jejuni isolates in Southern Spain. Microbiol Spectr 2024; 12:e0102824. [PMID: 39162511 PMCID: PMC11449230 DOI: 10.1128/spectrum.01028-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/09/2024] [Indexed: 08/21/2024] Open
Abstract
Campylobacter jejuni is the main cause of bacterial gastroenteritis and a public health problem worldwide. Little information is available on the genotypic characteristics of human C. jejuni in Spain. This study is based on an analysis of the resistome, virulome, and phylogenetic relationship, antibiogram prediction, and antimicrobial susceptibility of 114 human isolates of C. jejuni from a tertiary hospital in southern Spain from October 2020 to June 2023. The isolates were sequenced using Illumina technology, and a bioinformatic analysis was subsequently performed. The susceptibility of C. jejuni isolates to ciprofloxacin, tetracycline, and erythromycin was also tested. The resistance rates for each antibiotic were 90.3% for ciprofloxacin, 66.7% for tetracycline, and 0.88% for erythromycin. The fluoroquinolone resistance rate obtained is well above the European average (69.1%). CC-21 (n = 23), ST-572 (n = 13), and ST-6532 (n = 13) were the most prevalent clonal complexes (CCs) and sequence types (STs). In the virulome, the cadF, ciaB, and cdtABC genes were detected in all the isolates. A prevalence of 20.1% was obtained for the genes wlaN and cstIII, which are related to the pathogenesis of Guillain-Barré syndrome (GBS). The prevalence of the main antimicrobial resistance markers detected were CmeABC (92.1%), RE-cmeABC (7.9%), the T86I substitution in gyrA (88.9%), blaOXA-61 (72.6%), tet(O) (65.8%), and ant (6)-Ia (17.1%). High antibiogram prediction rates (>97%) were obtained, except for in the case of the erythromycin-resistant phenotype. This study contributes significantly to the knowledge of C. jejuni genomics for the prevention, treatment, and control of infections caused by this pathogen.IMPORTANCEDespite being the pathogen with the greatest number of gastroenteritis cases worldwide, Campylobacter jejuni remains a poorly studied microorganism. A sustained increase in fluoroquinolone resistance in human isolates is a problem when treating Campylobacter infections. The development of whole genome sequencing (WGS) techniques has allowed us to better understand the genotypic characteristics of this pathogen and relate them to antibiotic resistance phenotypes. These techniques complement the data obtained from the phenotypic analysis of C. jejuni isolates. The zoonotic transmission of C. jejuni through the consumption of contaminated poultry supports approaching the study of this pathogen through "One Health" approach. In addition, due to the limited information on the genomic characteristics of C. jejuni in Spain, this study provides important data and allows us to compare the results with those obtained in other countries.
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Affiliation(s)
| | | | - Carlos S Casimiro-Soriguer
- Plataforma Andaluza de Medicina Computacional, Fundación Pública Andaluza Progreso y Salud, Sevilla, Spain
| | - Estefanía Jurado-Tarifa
- Instituto de Investigación e Innovación Biomédica de Cádiz (INIBICA), Hospital Universitario Puerta del Mar, Cádiz, Spain
| | - Federico Arroyo
- UGC Microbiología, Hospital Universitario Puerta del Mar, Cádiz, Spain
| | - María Lara
- Plataforma Andaluza de Medicina Computacional, Fundación Pública Andaluza Progreso y Salud, Sevilla, Spain
| | - J Alberto Chaves
- Subdirección de Protección de la Salud, Consejería de Salud y Familias, Sevilla, Spain
| | - Joaquín Dopazo
- Plataforma Andaluza de Medicina Computacional, Fundación Pública Andaluza Progreso y Salud, Sevilla, Spain
| | - Manuel A Rodríguez-Iglesias
- UGC Microbiología, Hospital Universitario Puerta del Mar, Cádiz, Spain
- Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz, Cádiz, Spain
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12
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Ferreira R, Pinto G, Presa E, Oleastro M, Silva C, Vieira L, Sousa C, Pires DP, Figueiredo C, Melo LDR. Screening and in silico characterization of prophages in Helicobacter pylori clinical strains. Microbes Infect 2024:105429. [PMID: 39368610 DOI: 10.1016/j.micinf.2024.105429] [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: 05/16/2024] [Revised: 10/02/2024] [Accepted: 10/02/2024] [Indexed: 10/07/2024]
Abstract
The increase of antibiotic resistance calls for alternatives to control Helicobacter pylori, a Gram-negative bacterium associated with various gastric diseases. Bacteriophages (phages) can be highly effective in the treatment of pathogenic bacteria. Here, we develop a method to identify prophages in H. pylori genomes aiming at a future use in therapy. A PCR-based technique tested five primer pairs on 74 clinical H. pylori strains. With the PCR screening, 14 strains most likely to carry prophages were fully sequenced. After that, a more holistic approach was taken by studying the complete genome of the strains. The work allowed us to identify 12 intact prophage sequences, which were then characterized concerning their morphology, virulence, and antibiotic-resistance genes. To understand the variability of prophages, a phylogenetic analysis using the sequences of all H. pylori phages reported to date was performed. Using a PCR-based technique we increased the efficiency of identifying complete prophages to 54.1 %. Genes with homology to potential virulence factors were identified in some new prophages. Phylogenetic analysis revealed a close relationship among H. pylori-phages, although there are phages with different geographical origins. This study provides a deeper understanding of H. pylori-phages, providing valuable insights into their potential use in therapy.
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Affiliation(s)
- Rute Ferreira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal; i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Graça Pinto
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Eva Presa
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Mónica Oleastro
- Department of Infectious Diseases, National Institute of Health Doctor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Catarina Silva
- Unit of Technology and Innovation, Department of Human Genetics, National Institute of Health Doctor Ricardo Jorge (INSA), Lisbon, Portugal; Centre for Toxicogenomics and Human Health (ToxOmics), NOVA Medical School, Faculdade de Ciências Médicas, University Nova de Lisboa, Lisbon, Portugal
| | - Luís Vieira
- Unit of Technology and Innovation, Department of Human Genetics, National Institute of Health Doctor Ricardo Jorge (INSA), Lisbon, Portugal; Centre for Toxicogenomics and Human Health (ToxOmics), NOVA Medical School, Faculdade de Ciências Médicas, University Nova de Lisboa, Lisbon, Portugal
| | - Cláudia Sousa
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Diana P Pires
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal; LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Ceu Figueiredo
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal; Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal; Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Luís D R Melo
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal; LABBELS -Associate Laboratory, Braga, Guimarães, Portugal.
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Luo Y, Payne M, Kaur S, Octavia S, Lan R. Genomic evidence of two-staged transmission of the early seventh cholera pandemic. Nat Commun 2024; 15:8504. [PMID: 39353924 PMCID: PMC11445481 DOI: 10.1038/s41467-024-52800-w] [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: 02/25/2024] [Accepted: 09/19/2024] [Indexed: 10/03/2024] Open
Abstract
The seventh cholera pandemic started in 1961 in Indonesia and spread across the world in three waves in the decades that followed. Here, we utilised genomic evidence to detail the first wave of the seventh pandemic. Genomes of 22 seventh pandemic Vibrio cholerae isolates from 1961 to 1979 were completely sequenced. Together with 152 publicly available genomes from the same period, they fell into seven phylogenetic clusters (CL1-CL7). By multilevel genome typing (MGT), all were assigned to MGT2 ST1 (Wave 1) except three isolates in CL7 which were typed as MGT2 ST2 (Wave 2). The Wave 1 seventh pandemic expanded in two stages, with Stage 1 (CL1-CL5) spread across Asia and Stage 2 (CL6 and CL7) spread to the Middle East and Africa. Three non-synonymous mutations, one each, in three regulatory genes, csrD (global regulator), acfB (chemotaxis), and luxO (quorum sensing) may have critically contributed to its pandemicity. The three MGT2 ST2 isolates in CL7 were the progenitors of Wave 2 and evolved from within Wave 1 with acquisition of a novel IncA/C plasmid. Our findings provide new insight into the evolution and transmission of the early seventh pandemic, which may aid future cholera prevention and control.
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Affiliation(s)
- Yun Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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14
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Gong Y, Feng Y, Zong Z, Lv X. Characterization of a KPC-84 harboring Klebsiella pneumoniae ST11 clinical isolate with ceftazidime-avibactam resistance. Eur J Clin Microbiol Infect Dis 2024; 43:2029-2035. [PMID: 39110337 DOI: 10.1007/s10096-024-04910-y] [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: 03/14/2024] [Accepted: 07/24/2024] [Indexed: 09/18/2024]
Abstract
A novel KPC variant, KPC-84, identified in a Klebsiella pneumoniae isolate from China, exhibits a threonine (T) to proline (P) amino acid substitution at Ambler position 243(T243P), altering from the KPC-2 sequence. Cloning and expression of blaKPC-84 in Escherichia coli, with subsequent MIC assessments, revealed increased resistance to ceftazidime-avibactam and significantly reduced carbapenemase activity compared to KPC-2. Kinetic measurements showed that KPC-84 exhibited sligthly higher hydrolysis of ceftazidime and reduced affinity for avibactam compared to KPC-2. This study emphasizes the emerging diversity of KPC variants with ceftazidime-avibactam resistance, underscoring the complexity of addressing carbapenem-resistant Klebsiella pneumoniae infections.
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Affiliation(s)
- Yanqiao Gong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Department of Infection Control, Minda Hospital, Hubei Minzu University, Enshi, China
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Xiaoju Lv
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.
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Rahim K, Nawaz MN, Almehmadi M, Alsuwat MA, Liu L, Yu C, Khan SS. Public health implications of antibiotic resistance in sewage water: an epidemiological perspective. BIORESOUR BIOPROCESS 2024; 11:91. [PMID: 39340706 PMCID: PMC11438758 DOI: 10.1186/s40643-024-00807-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024] Open
Abstract
The emergence and rapid spread of antibiotic resistance pose a major threat to global health, attributing to misuse and overuse of antibiotics resulting in antibiotics-resistant bacteria through natural mutation or transfer of resistance genes. A cross-sectional study was carried out, in which a total of 36 samples were systematically collected; of these, 26 were derived from the wastewater efflux and 10 from the receiving waters at several critical junctures along the Sutlej River. Herein, this study elucidated elevated levels of antibiotic resistance among bacterial isolates sourced from urban wastewater. Escherichia coli (E. coli) was the highest at 90% among the isolates, followed by Klebsiella pneumoniae (K. pneumoniae) at 58%, Pseudomonas aeruginosa (P. aeruginosa) at 55%, and Salmonella spp. at 53%. Many antibiotics were found to be more resistant including Ciproflaxacin, Co-Trimaxazole, Ampicillin and Tetracycline. Several antibiotic-resistance genes were found in isolated bacterial spp., such as Aminoglycosides (aadA), Sulfonamides (Sul1, Sul3), Tetracyclines (Tet (A/B/D)) and Cephalosporins (Bla_CTM X) at 41%, 35%, 29% and 12% respectively. Furthermore, the development of innovative wastewater treatment models and surveillance programs are crucial to counteract the dissemination of antibiotic resistance. To investigate the genetic determinants of antibiotic resistance, molecular analysis was performed, including DNA isolation, PCR amplification, and sequence analysis. The study helps investigate a diverse range of ARBs and ARGs in wastewater, which highlights the need of better laws for antibiotic usage and wastewater treatment processes. This investigation also stresses on regular monitoring of ARBs and ARGs in sewage wastewater. Through proactive interventions and sustained scientific inquiry, we can strive toward preserving environmental integrity and public health for successive generations.
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Affiliation(s)
- Kashif Rahim
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Muhammad Naveed Nawaz
- Department of Biological Sciences and Technology, China University of Geosciences, Wuhan, China
| | - Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Meshari A Alsuwat
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Luo Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shahin Shah Khan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Chen Y, Huang J, Dong L, Xu B, Li L, Zhao Z, Li B. Clinical and genomic characterization of carbapenem-resistant Enterobacterales bloodstream infections in patients with hematologic malignancies. Front Cell Infect Microbiol 2024; 14:1471477. [PMID: 39391886 PMCID: PMC11464489 DOI: 10.3389/fcimb.2024.1471477] [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: 07/27/2024] [Accepted: 09/06/2024] [Indexed: 10/12/2024] Open
Abstract
Background Carbapenem-resistant Enterobacterales (CRE) bloodstream infections (BSIs) pose a significant risk to patients with hematologic malignancies, yet the distinct features and outcomes of these infections are not thoroughly understood. Methods This retrospective study examined the characteristics and clinical outcomes of patients with Enterobacterales BSIs at the Hematology Department of Fujian Medical University Union Hospital from 2018 to 2022. Whole-genome sequencing was conducted on 45 consecutive CRE BSI isolates during this period. Results A total of 301 patients with Enterobacterales BSIs were included, with 65 (21.6%) cases of CRE and 236 (78.4%) cases of carbapenem-susceptible Enterobacterales (CSE). CRE infections accounted for 16.9% to 26.9% of all Enterobacterales BSIs, and carbapenem-resistant Klebsiella pneumoniae (CRKP) was the predominant strain. The most frequent sequence type (ST) and carbapenemase among CRKP were ST11 (68.6%) and blaKPC-2 (80.0%), respectively. Perianal infections, multiple infection foci, and a history of multiple hospitalizations, ICU stays, and prior CRE infections were identified as risk factors for CRE BSIs. Patients in the CRE group experienced significantly higher proportions of infection-related septic shock (43.1% vs. 19.9%, P < 0.0003) and 30-day all-cause mortality (56.9% vs. 24.6%, P < 0.0001) compared to those in the CSE group. Patient's age and disease subtypes, strain subtypes, and antimicrobial treatment regimens significantly influenced survival in patients with CRE BSIs. Conclusions CRE BSIs are a frequent complication in patients with hematological malignancies undergoing treatment and are associated with poor survival rates. A comprehensive understanding of risk factors and ongoing surveillance of prevalent strains are essential for the effective management of these infections.
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Affiliation(s)
- Yi Chen
- Fujian Medical University Union Hospital, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fuzhou, China
| | - Jiangqing Huang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Luyan Dong
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Binbin Xu
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Lei Li
- Department of Clinical Laboratory, Fujian Medical University Union Hospital Pingtan Branch, Fuzhou, China
| | - Zhichang Zhao
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, China
| | - Bin Li
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
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17
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Gelalcha BD, Mohamed RI, Gelgie AE, Kerro Dego O. Molecular epidemiology of extended-spectrum beta-lactamase-producing- Klebsiella species in East Tennessee dairy cattle farms. Front Microbiol 2024; 15:1439363. [PMID: 39380685 PMCID: PMC11458399 DOI: 10.3389/fmicb.2024.1439363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/30/2024] [Indexed: 10/10/2024] Open
Abstract
Introduction The rising prevalence of Extended-Spectrum Beta-Lactamase (ESBL)-producing Klebsiella species (spp.) poses a significant threat to human and animal health and environmental safety. To address this pressing issue, a comprehensive study was undertaken to elucidate the burden and dissemination mechanisms of ESBL-Klebsiella spp. in dairy cattle farms. Methods Fifty-seven Klebsiella species were isolated on CHROMagar™ ESBL plates and confirmed with MADLI-TOF MS and whole genome sequenced from 14 dairy farms. Results and discussion Six families of beta-lactamase (bla) (bla CTX-M, bla SHV, bla TEM, bla OXY, bla OXA, and bla SED) were detected in ESBL-Klebsiella spp. genomes. Most (73%) of isolates had the first three types of beta-lactamase genes, with bla SHV being the most frequent, followed by bla CTX-M. Most (93%) isolates harbored two or more bla genes. The isolates were genotypically MDR, with 26 distinct types of antibiotic resistance genes (ARGs) and point mutations in gyrA, gyrB, and parC genes. The genomes also harbored 22 different plasmid replicon types, including three novel IncFII. The IncFII and Col440I plasmids were the most frequent and were associated with bla CTXM-27 and qnrB19 genes, respectively. Eighteen distinct sequence types (STs), including eight isolates with novel STs of K. pneumoniae, were detected. The most frequently occurring STs were ST353 (n = 8), ST469 (n = 6), and the novel ST7501 (n = 6). Clusters of ESBL-Klebsiella strains with identical STs, plasmids, and ARGs were detected in multiple farms, suggesting possible clonal expansion. The same ESBL variant was linked to identical plasmids in different Klebsiella STs in some farms, suggesting horizontal spread of the resistance gene. The high burden and dual spread mechanism of ESBL genes in Klebsiella species, combined with the emergence of novel sequence types, could swiftly increase the prevalence of ESBL-Klebsiella spp., posing significant risks to human, animal, and environmental health. Immediate action is needed to implement rigorous surveillance and control measures to mitigate this risk.
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Affiliation(s)
- Benti D. Gelalcha
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
| | - Ruwaa I. Mohamed
- Department of Genome Science and Technology, The University of Tennessee, Knoxville, TN, United States
| | - Aga Edema Gelgie
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
| | - Oudessa Kerro Dego
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
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Cornu Hewitt B, Bossers A, van Kersen W, de Rooij MMT, Smit LAM. Associations between acquired antimicrobial resistance genes in the upper respiratory tract and livestock farm exposures: a case-control study in COPD and non-COPD individuals. J Antimicrob Chemother 2024:dkae335. [PMID: 39315772 DOI: 10.1093/jac/dkae335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
BACKGROUND Livestock-related emissions have been associated with aggravations of respiratory symptoms in patients with chronic obstructive pulmonary disease (COPD), potentially by altering the respiratory resistome. OBJECTIVES This study investigates the structure of the acquired oropharyngeal (OP) resistome of patients with COPD and controls, its interplay with the respiratory microbiome and associations with residential livestock exposure. METHODS In a matched case-control study in the rural Netherlands, we analysed OP swabs from 35 patients with COPD and 34 controls, none of whom had used antibiotics in the preceding 4 weeks. Resistome profiling was performed using ResCap, complemented by prior characterization of the microbiome via 16S rRNA-based sequencing. Residential livestock farm exposure was defined using distance-based variables alongside modelled concentrations of livestock-emitted microbial pollutants. We compared resistome profiles between patients with COPD and controls, examining alpha and beta diversity as well as differential abundance. Additionally, we assessed the interplay between the resistome and microbiome using co-occurrence networks and Procrustes analysis. Variations in resistome profiles were also analysed based on residential livestock exposures. RESULTS Patients with COPD exhibited higher resistome diversity than controls (Shannon diversity, P = 0.047), though resistome composition remained similar between groups (PERMANOVA, P = 0.19). Significant correlations were observed between the OP resistome and microbiome compositions, with distinct patterns in co-occurrence networks. Residential exposure to livestock farms was not associated with resistome alterations. CONCLUSIONS Our findings reveal the COPD airway as a hospitable environment for antimicrobial resistance genes, irrespective of recent antimicrobial usage. Demonstrating the interplay between the resistome and microbiome, our study underscores the importance of a deeper understanding of the resistome in respiratory health.
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Affiliation(s)
- Beatrice Cornu Hewitt
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80178, Utrecht 3508 TD, The Netherlands
| | - Alex Bossers
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80178, Utrecht 3508 TD, The Netherlands
| | - Warner van Kersen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80178, Utrecht 3508 TD, The Netherlands
| | - Myrna M T de Rooij
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80178, Utrecht 3508 TD, The Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80178, Utrecht 3508 TD, The Netherlands
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Koncz M, Stirling T, Hadj Mehdi H, Méhi O, Eszenyi B, Asbóth A, Apjok G, Tóth Á, Orosz L, Vásárhelyi BM, Ari E, Daruka L, Polgár TF, Schneider G, Zalokh SA, Számel M, Fekete G, Bohár B, Nagy Varga K, Visnyovszki Á, Székely E, Licker MS, Izmendi O, Costache C, Gajic I, Lukovic B, Molnár S, Szőcs-Gazdi UO, Bozai C, Indreas M, Kristóf K, Van der Henst C, Breine A, Pál C, Papp B, Kintses B. Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens. Cell 2024:S0092-8674(24)01027-4. [PMID: 39332413 DOI: 10.1016/j.cell.2024.09.009] [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: 01/17/2024] [Revised: 05/15/2024] [Accepted: 09/04/2024] [Indexed: 09/29/2024]
Abstract
Phage therapy is gaining increasing interest in the fight against critically antibiotic-resistant nosocomial pathogens. However, the narrow host range of bacteriophages hampers the development of broadly effective phage therapeutics and demands precision approaches. Here, we combine large-scale phylogeographic analysis with high-throughput phage typing to guide the development of precision phage cocktails targeting carbapenem-resistant Acinetobacter baumannii, a top-priority pathogen. Our analysis reveals that a few strain types dominate infections in each world region, with their geographical distribution remaining stable within 6 years. As we demonstrate in Eastern Europe, this spatiotemporal distribution enables preemptive preparation of region-specific phage collections that target most local infections. Finally, we showcase the efficacy of phage cocktails against prevalent strain types using in vitro and animal infection models. Ultimately, genomic surveillance identifies patients benefiting from the same phages across geographical scales, thus providing a scalable framework for precision phage therapy.
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Affiliation(s)
- Mihály Koncz
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary
| | - Tamás Stirling
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary; Doctoral School of Biology, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - Hiba Hadj Mehdi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary; Doctoral School of Biology, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - Orsolya Méhi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Bálint Eszenyi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - András Asbóth
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary; Department of Genetics, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, 1117 Budapest, Hungary
| | - Gábor Apjok
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Ákos Tóth
- National Center for Public Health and Pharmacy, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | - László Orosz
- Department of Medical Microbiology, University of Szeged, Szent-Györgyi Albert Medical School, Dom tér 10, 6720 Szeged, Hungary
| | - Bálint Márk Vásárhelyi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Eszter Ari
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; Department of Genetics, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, 1117 Budapest, Hungary; HCEMM-BRC Metabolic Systems Biology Group, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Lejla Daruka
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Tamás Ferenc Polgár
- Institute of Biophysics, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; Theoretical Medicine Doctoral School, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - György Schneider
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Sif Aldin Zalokh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Mónika Számel
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Metabolic Systems Biology Group, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Balázs Bohár
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, 10th Floor Commonwealth Building Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Karolina Nagy Varga
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Ádám Visnyovszki
- South-Pest Central Hospital National Institute of Hematology and Infectious Diseases, Nagyvárad tér 1, 1097 Budapest, Hungary; Doctoral School of Interdisciplinary Medical Sciences, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - Edit Székely
- George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, Str. Gheorghe Marinescu 38, 540142 Targu Mures, Romania; County Emergency Clinical Hospital of Targu Mures, Str. Dr. Gh. Marinescu 50, 540136 Targu Mures, Romania
| | - Monica-Sorina Licker
- Microbiology Department, Multidisciplinary Research Center on Antimicrobial Resistance, "Victor Babes" University of Medicine and Pharmacy, Str. Eftimie Murgu 2, 300041 Timisoara, Romania; Microbiology Laboratory, "Pius Branzeu" Emergency Clinical County Hospital, Str. Liviu Rebreanu 156, 300723 Timisoara, Romania
| | - Oana Izmendi
- Microbiology Department, Multidisciplinary Research Center on Antimicrobial Resistance, "Victor Babes" University of Medicine and Pharmacy, Str. Eftimie Murgu 2, 300041 Timisoara, Romania; Microbiology Laboratory, "Pius Branzeu" Emergency Clinical County Hospital, Str. Liviu Rebreanu 156, 300723 Timisoara, Romania; Doctoral School, "Victor Babes" University of Medicine and Pharmacy, Str. Eftimie Murgu 2, 300041 Timisoara, Romania
| | - Carmen Costache
- Department of Microbiology, University of Medicine and Pharmacy "Iuliu Hatieganu" Cluj-Napoca, Str. Victor Babes 8, 400347 Cluj-Napoca, Romania
| | - Ina Gajic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Dr Subotica 8, 11000 Belgrade, Serbia
| | - Bojana Lukovic
- Academy of Applied Studies Belgrade, College of Health Sciences, Bulevar Zorana Djindjica 152a, Belgrade, Serbia
| | - Szabolcs Molnár
- Emergency County Hospital Miercurea-Ciuc, Str. Doctor Dénes László 2, 530173 Miercurea Ciuc, Romania
| | | | - Csilla Bozai
- County Emergency Hospital Satu Mare, Str. Ravensburg 1-3, 440192 Satu Mare, Romania
| | - Marina Indreas
- Bacau County Emergency Hospital, Str. Haret Spiru 2-4, 600114 Bacau, Romania
| | - Katalin Kristóf
- Institute of Laboratory Medicine, Semmelweis University, Üllői út 78/b, 1083 Budapest, Hungary
| | - Charles Van der Henst
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, Pleinlaan 2, Building E-3, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Elsene, 1050 Brussels, Belgium
| | - Anke Breine
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, Pleinlaan 2, Building E-3, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Elsene, 1050 Brussels, Belgium
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Metabolic Systems Biology Group, Temesvári Krt. 62, 6726 Szeged, Hungary; National Laboratory for Health Security, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary.
| | - Bálint Kintses
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary.
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20
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Trung NV, Zaw Moe A, May Than H, Bich Chieu TT, Mukarram Hossain ASM, Trung Thanh N, Yen HX, Yen PLK, Nghia NH, Murray GGR, Su Wai T, Thein Maw M, Myint HT, Win YT, Wood J, Thwaites G, Maskell DJ, Tucker AW, Hoa NT. Prevalence, antimicrobial resistance and genomic comparison of non-typhoidal salmonella isolated from pig farms with different levels of intensification in Yangon Region, Myanmar. PLoS One 2024; 19:e0307868. [PMID: 39298421 DOI: 10.1371/journal.pone.0307868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 07/14/2024] [Indexed: 09/21/2024] Open
Abstract
In Myanmar, where backyard, semi-intensive, and intensive pig (Sus scrofa domesticus) farming coexist, there is limited understanding of the zoonotic risks and antimicrobial resistance (AMR) associated with these farming practices. This study was conducted to investigate the prevalence, AMR and genomic features of Salmonella in pig farms in the Yangon region and the impact of farm intensification to provide evidence to support risk-based future management approaches. Twenty-three farms with different production scales were sampled for two periods with three sampling-visit each. Antimicrobial susceptibility tests and whole-genome sequencing were performed on the isolates. The prevalence of Salmonella was 44.5% in samples collected from backyard farms, followed by intensive (39.5%) and semi-intensive farms (19.5%). The prevalence of multi-drug resistant isolates from intensive farms (45/84, 53.6%) was higher than those from backyard (32/171, 18.7%) and semi-intensive farms (25/161, 15.5%). Among 28 different serovars identified, S. Weltevreden (40; 14.5%), S. Kentucky (38; 13.8%), S. Stanley (35, 12.7%), S. Typhimurium (22; 8.0%) and S. Brancaster (20; 7.3%) were the most prevalent serovars and accounted for 56.3% of the genome sequenced strains. The diversity of Salmonella serovars was highest in semi-intensive and backyard farms (21 and 19 different serovars, respectively). The high prevalence of globally emerging S. Kentucky ST198 was detected on backyard farms. The invasive-infection linked typhoid-toxin gene (cdtB) was found in the backyard farm isolated S. Typhimurium, relatively enriched in virulence and AMR genes, presented an important target for future surveillance. While intensification, in terms of semi-intensive versus backyard production, maybe a mitigator for zoonotic risk through a lower prevalence of Salmonella, intensive production appears to enhance AMR-associated risks. Therefore, it remains crucial to closely monitor the AMR and virulence potential of this pathogen at all scales of production. The results underscored the complex relationship between intensification of animal production and the prevalence, diversity and AMR of Salmonella from pig farms in Myanmar.
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Affiliation(s)
- Nguyen Vinh Trung
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Faculty of Veterinary Medicine, College of Agriculture, Can Tho University, Can Tho, Vietnam
| | - Aung Zaw Moe
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Hlaing May Than
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | | | - A S Md Mukarram Hossain
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, University of Manchester, Alderley Park, Macclesfield, United Kingdom
| | | | - Huynh Xuan Yen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phung Le Kim Yen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Nghia
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Thiri Su Wai
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Min Thein Maw
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Hnin Thidar Myint
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Ye Tun Win
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - James Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom
- Microbiology Department and Center for BioMedicine Research, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
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21
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Girault G, Freddi L, Jay M, Perrot L, Dremeau A, Drapeau A, Delannoy S, Fach P, Ferreira Vicente A, Mick V, Ponsart C, Djokic V. Combination of in silico and molecular techniques for discrimination and virulence characterization of marine Brucella ceti and Brucella pinnipedialis. Front Microbiol 2024; 15:1437408. [PMID: 39360323 PMCID: PMC11444999 DOI: 10.3389/fmicb.2024.1437408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 08/23/2024] [Indexed: 10/04/2024] Open
Abstract
Introduction Mammals are the main hosts for Brucella sp., agents of worldwide zoonosis. Marine cetaceans and pinnipeds can be infected by Brucella ceti and B. pinnipedialis, respectively. Besides classical bacteriological typing, molecular approaches such as MLVA, MLSA, and whole-genome sequencing (WGS) can differentiate these species but are cumbersome to perform. Methods We compared the DNA and genome sequences of 12 strains isolated from nine marine mammals, with highly zoonotic B. melitensis, B. abortus, and B. suis, and the publicly available genomes of B. ceti and B. pinnipedialis. In silico pipelines were used to detect the antimicrobial resistance (AMR), plasmid, and virulence genes (VGs) by screening six open-source and one home-made library. Results and discussion Our results show that easier-to-use HRM-PCR, Bruce-ladder, and Suis-ladder can separate marine Brucella sp., and the results are fully concordant with other molecular methods, such as WGS. However, the restriction fragment length polymorphism (RFLP) method cannot discriminate between B. pinnipedialis and B. ceti B1-94-like isolates. MLVA-16 results divided the investigated strains into three clades according to their preferred host, which was confirmed in WGS. In silico analysis did not find any AMR and plasmid genes, suggesting antimicrobial susceptibility of marine Brucella, while the presence of the VGs btpA gene was variable dependent on the clade. Conclusion The HRM-PCR and Suis-ladder are quick, easy, and cost-effective methods to identify marine Brucella sp. Moreover, in silico genome analyses can give useful insights into the genetic virulence and pathogenicity potential of marine Brucella strains.
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Affiliation(s)
- Guillaume Girault
- Animal Health Laboratory, EU/WOAH and National Reference Laboratory for Brucellosis, Anses/Paris-Est University, Maisons-Alfort, France
| | - Luca Freddi
- Animal Health Laboratory, EU/WOAH and National Reference Laboratory for Brucellosis, Anses/Paris-Est University, Maisons-Alfort, France
| | - Maryne Jay
- Animal Health Laboratory, EU/WOAH and National Reference Laboratory for Brucellosis, Anses/Paris-Est University, Maisons-Alfort, France
| | - Ludivine Perrot
- Animal Health Laboratory, EU/WOAH and National Reference Laboratory for Brucellosis, Anses/Paris-Est University, Maisons-Alfort, France
| | - Alexandre Dremeau
- Animal Health Laboratory, EU/WOAH and National Reference Laboratory for Brucellosis, Anses/Paris-Est University, Maisons-Alfort, France
| | - Antoine Drapeau
- Animal Health Laboratory, EU/WOAH and National Reference Laboratory for Brucellosis, Anses/Paris-Est University, Maisons-Alfort, France
| | - Sabine Delannoy
- IdentyPath Genomics Platform, Food Safety Laboratory, ANSES, Maisons-Alfort, France
| | - Patrick Fach
- IdentyPath Genomics Platform, Food Safety Laboratory, ANSES, Maisons-Alfort, France
| | - Acacia Ferreira Vicente
- Animal Health Laboratory, EU/WOAH and National Reference Laboratory for Brucellosis, Anses/Paris-Est University, Maisons-Alfort, France
| | - Virginie Mick
- Animal Health Laboratory, EU/WOAH and National Reference Laboratory for Brucellosis, Anses/Paris-Est University, Maisons-Alfort, France
| | - Claire Ponsart
- Animal Health Laboratory, EU/WOAH and National Reference Laboratory for Brucellosis, Anses/Paris-Est University, Maisons-Alfort, France
| | - Vitomir Djokic
- Animal Health Laboratory, EU/WOAH and National Reference Laboratory for Brucellosis, Anses/Paris-Est University, Maisons-Alfort, France
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Guéneau V, Jiménez G, Castex M, Briandet R. Insights into the genomic and phenotypic characteristics of Bacillus spp. strains isolated from biofilms in broiler farms. Appl Environ Microbiol 2024; 90:e0066324. [PMID: 39158314 PMCID: PMC11409695 DOI: 10.1128/aem.00663-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024] Open
Abstract
The characterization of surface microbiota living in biofilms within livestock buildings has been relatively unexplored, despite its potential impact on animal health. To enhance our understanding of these microbial communities, we characterized 11 spore-forming strains isolated from two commercial broiler chicken farms. Sequencing of the strains revealed them to belong to three species Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis. Genomic analysis revealed the presence of antimicrobial resistance genes and genes associated with antimicrobial secretion specific to each species. We conducted a comprehensive characterization of the biofilm formed by these strains under various conditions, and we revealed significant structural heterogeneity across the different strains. A macro-colony interaction model was employed to assess the compatibility of these strains to coexist in mixed biofilms. We identified highly competitive B. velezensis strains, which cannot coexist with other Bacillus spp. Using confocal laser scanning microscopy along with a specific dye for extracellular DNA, we uncovered the importance of extracellular DNA for the formation of B. licheniformis biofilms. Altogether, the results highlight the heterogeneity in both genome and biofilm structure among Bacillus spp. isolated from biofilms present within livestock buildings.IMPORTANCELittle is known about the microbial communities that develop on farms in direct contact with animals. Nonpathogenic strains of Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis were found in biofilm samples collected from surfaces in contact with animals. Significant genetic and phenotypic diversity was described among these Bacillus strains. The strains do not possess mobile antibiotic resistance genes in their genomes and have a strong capacity to form structured biofilms. Among these species, B. velezensis was noted for its high competitiveness compared with the other Bacillus spp. Additionally, the importance of extracellular DNA in the formation of B. licheniformis biofilms was observed. These findings provide insights for the management of these surface microbiota that can influence animal health, such as the use of competitive strains to minimize the establishment of undesirable bacteria or enzymes capable of specifically deconstructing biofilms.
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Affiliation(s)
- Virgile Guéneau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Lallemand SAS, Blagnac, France
| | | | | | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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Lee YQ, Sri La Sri Ponnampalavanar S, Wong JH, Kong ZX, Ngoi ST, Karunakaran R, Lau MY, Abdul Jabar K, Teh CSJ. Investigation on the mechanisms of carbapenem resistance among the non-carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae. Front Cell Infect Microbiol 2024; 14:1464816. [PMID: 39359938 PMCID: PMC11445613 DOI: 10.3389/fcimb.2024.1464816] [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: 07/15/2024] [Accepted: 08/26/2024] [Indexed: 10/04/2024] Open
Abstract
Background In Malaysia, an increase in non-carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae (NC-CRKP) has been observed over the years. Previously, four NC-CRKP with increased susceptibility to ciprofloxacin in the presence of phenylalanine-arginine β-naphthylamide (PAβN) were identified. However, no contribution of the PAβN-inhibited efflux pump to carbapenem resistance was observed. All four NC-CRKP harboured non-carbapenemase β-lactamase, with two also exhibiting porin loss. In this study, we further investigated the genomic features and resistance mechanisms of these four isolates. Methods All four NC-CRKP were subjected to whole-genome sequencing, followed by comparative genomic and phylogenetic analyses. Results Multi-locus sequence typing (MLST) analysis divided the four NC-CRKP into different sequence types: ST392, ST45, ST14, and ST5947. Neither major nor rare carbapenemase genes were detected. Given the presence of non-carbapenemase β-lactamase in all isolates, we further investigated the potential mechanisms of resistance by identifying related chromosomal mutations. Deletion mutation was detected in the cation efflux system protein CusF. Insertion mutation was identified in the nickel/cobalt efflux protein RcnA. Missense mutation of ompK36 porin was detected in two isolates, while the loss of ompK36 porin was observed in another two isolates. Conclusions This study revealed that NC-CRKP may confer carbapenem resistance through a combination of non-carbapenemase β-lactamase and potential chromosomal mutations including missense mutation or loss of ompK36 porin and/or a frameshift missense mutation in efflux pump systems, such as cation efflux system protein CusF and nickel/cobalt efflux protein RcnA. Our findings highlighted the significance of implementing whole-genome sequencing into clinical practice to promote the surveillance of carbapenem resistance mechanisms among NC-CRKP.
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Affiliation(s)
- Yee Qing Lee
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | - Jia Haw Wong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Zhi Xian Kong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Soo Tein Ngoi
- Department of Anaesthesiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Rina Karunakaran
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Min Yi Lau
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Kartini Abdul Jabar
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Cindy Shuan Ju Teh
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
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Zhang X, Xie Y, Zhang Y, Lei T, Zhou L, Yao J, Liu L, Liu H, He J, Yu Y, Tu Y, Li X. Evolution of ceftazidime-avibactam resistance driven by mutations in double-copy blaKPC-2 to blaKPC-189 during treatment of ST11 carbapenem-resistant Klebsiella pneumoniae. mSystems 2024:e0072224. [PMID: 39287378 DOI: 10.1128/msystems.00722-24] [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: 05/28/2024] [Accepted: 08/29/2024] [Indexed: 09/19/2024] Open
Abstract
Klebsiella pneumoniae carbapenemase (KPC) variants can contribute to resistance to ceftazidime-avibactam (CZA) in Klebsiella pneumoniae (KP). However, two-copy KPC variant-mediated resistance to CZA has rarely been reported to date. Here, we aimed to clarify the evolutionary trajectory of CZA resistance driven by mutations in double-copy blaKPC-2 to blaKPC-189 carried by the tandem core structure (ISKpn6-blaKPC-ISKpn27-tnpR-IS26) during treatment of ST11 carbapenem-resistant K. pneumoniae (CRKP). The CZA-resistant KP strain carried double-copy blaKPC-189, a variant with alanine-threonine and aspartate-tyrosine substitutions at Ambler amino acid positions 172 (A172T) and 179 (D179Y) of blaKPC-2. Clone experiments confirmed that, compared with that of the wild-type blaKPC-2 clone strain, the minimum inhibitory concentration of CZA increased 16-fold in the blaKPC-189-mutant strain. Furthermore, protein structure analysis revealed the A172T and D179Y mutations of blaKPC-189 can have a direct effect on the binding affinity of CAZ and AVI for KPC. Sequence comparison revealed that blaKPC-189 was mutated in a double-copy format upon CZA exposure, which was carried by the IS26-mediated tandem core structure ISKpn27-blaKPC-ISKpn6. This tandem core structure apparently evolves in vivo during infection, although not by self-transferring, and multiple ISKpn27-blaKPC-ISKpn6 copy numbers could mediate transferable CZA resistance upon mobilization. In addition, compared with the wild-type blaKPC-2 gene, the blaKPC-189 gene had no fitness cost. In summary, our study highlighted the emergence of CZA-resistant blaKPC-189 variants in the ST11 clone and the presence of a double-copy blaKPC-189 in the IncFII-type plasmid, which is carried by a tandem core structure (IS26-ISKpn6-blaKPC-189-ISKpn27-tnpR-IS26). IMPORTANCE To date, ceftazidime-avibactam (CZA) resistance caused by double-copy Klebsiella pneumoniae carbapenemase (KPC) variants has not been elucidated. The multicopy forms of carbapenem resistance genes carried by the same plasmid are relatively rare in most carbapenem-resistant Enterobacteriaceae. In this study, we elucidate the evolutionary trajectory of CZA resistance in ST11 carbapenem-resistant K. pneumoniae harboring a double-copy blaKPC and provide new insights into the mechanisms of acquired resistance to CZA.
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Affiliation(s)
- Xiaofan Zhang
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Clinical Laboratory, Feicheng Hospital of Traditional Chinese Medicine, Feicheng, Shandong, China
| | - Yinrong Xie
- Department of Clinical Laboratory, Xiamen Hospital of Traditional Chinese Medicine, Xiamen, Fujian, China
| | - Ying Zhang
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Tailong Lei
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Longjie Zhou
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jiayao Yao
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Lin Liu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haiyang Liu
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jintao He
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yunsong Yu
- Center for General Practice Medicine, Department of Infectious Diseases, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yuexing Tu
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Critical Care Medicine, Tongde Hospital of Zhejiang Province, 234 Gucui Road, Hangzhou, Zhejiang, China
| | - Xi Li
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
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Garner E, Maile-Moskowitz A, Angeles LF, Flach CF, Aga DS, Nambi I, Larsson DGJ, Bürgmann H, Zhang T, Vikesland PJ, Pruden A. Metagenomic Profiling of Internationally Sourced Sewage Influents and Effluents Yields Insight into Selecting Targets for Antibiotic Resistance Monitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:16547-16559. [PMID: 39229966 PMCID: PMC11411718 DOI: 10.1021/acs.est.4c03726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
It has been debated whether wastewater treatment plants (WWTPs) primarily act to attenuate or amplify antibiotic resistance genes (ARGs). However, ARGs are highly diverse with respect to their resistance mechanisms, mobilities, and taxonomic hosts and therefore their behavior in WWTPs should not be expected to be universally conserved. We applied metagenomic sequencing to wastewater influent and effluent samples from 12 international WWTPs to classify the behavior of specific ARGs entering and exiting WWTPs. In total, 1079 different ARGs originating from a variety of bacteria were detected. This included ARGs that could be mapped to assembled scaffolds corresponding to nine human pathogens. While the relative abundance (per 16S rRNA gene) of ARGs decreased during treatment at 11 of the 12 WWTPs sampled and absolute abundance (per mL) decreased at all 12 WWTPs, increases in relative abundance were observed for 40% of the ARGs detected at the 12th WWTP. Also, the relative abundance of mobile genetic elements (MGE) increased during treatment, but the fraction of ARGs known to be transmissible between species decreased, thus demonstrating that increased MGE prevalence may not be generally indicative of an increase in ARGs. A distinct conserved resistome was documented in both influent and effluent across samples, suggesting that well-functioning WWTPs generally attenuate influent antibiotic resistance loads. This work helps inform strategies for wastewater surveillance of antibiotic resistance, highlighting the utility of tracking ARGs as indicators of treatment performance and relative risk reduction.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Ayella Maile-Moskowitz
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Luisa F Angeles
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | - Carl-Fredrik Flach
- Institute of Biomedicine, Department of Infectious Diseases, Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Västra Götaland, SE-405 30 Gothenburg, Sweden
| | - Diana S Aga
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | - Indumathi Nambi
- Department of Civil Engineering, Indian Institute of Technology, Madras, Chennai 600036, India
| | - D G Joakim Larsson
- Institute of Biomedicine, Department of Infectious Diseases, Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Västra Götaland, SE-405 30 Gothenburg, Sweden
| | - Helmut Bürgmann
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum CH-6047, Switzerland
| | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam 999077, Hong Kong
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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Sung K, Nawaz M, Park M, Chon J, Khan SA, Alotaibi K, Khan AA. Comprehensive Genomic Analysis of Uropathogenic E. coli: Virulence Factors, Antimicrobial Resistance, and Mobile Genetic Elements. Pathogens 2024; 13:794. [PMID: 39338985 PMCID: PMC11434687 DOI: 10.3390/pathogens13090794] [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: 08/09/2024] [Revised: 08/26/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024] Open
Abstract
Our whole-genome sequencing analysis of sixteen uropathogenic E. coli isolates revealed a concerning picture of multidrug resistance and potentially virulent bacteria. All isolates belonged to four distinct clonal groups, with the highly prevalent ST131 lineage being associated with extensive antibiotic resistance and virulence factors. Notably, all isolates exhibited multidrug resistance, with some resistant to as many as 12 antibiotics. Fluoroquinolone resistance stemmed primarily from efflux pumps and mutations in gyrase and topoisomerase genes. Additionally, we identified genes encoding resistance to extended-spectrum cephalosporins, trimethoprim/sulfamethoxazole, and various heavy metals. The presence of diverse plasmids and phages suggests the potential for horizontal gene transfer and the dissemination of virulence factors. All isolates harbored genomic islands containing virulence factors associated with adhesion, biofilm formation, and invasion. Genes essential for iron acquisition, flagella biosynthesis, secretion systems, and toxin production were also prevalent. Adding further complexity to understanding the isolates' genetic makeup, we identified CRISPR-Cas systems. This study underscores the need for continued genomic surveillance in understanding the pathogenic mechanisms and resistance profiles of uropathogenic E. coli to aid in developing targeted therapeutic strategies.
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Affiliation(s)
- Kidon Sung
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Mohamed Nawaz
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Miseon Park
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Jungwhan Chon
- Department of Companion Animal Health, Inje University, Gimhae 50834, Republic of Korea
| | - Saeed A Khan
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Khulud Alotaibi
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Ashraf A Khan
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
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Berwa A, Caspar Y. Easy analysis of bacterial whole-genome sequencing data for clinical microbiologists using open-source Galaxy Platform: characterization of ESBL-producing Enterobacterales from bloodstream infections. J Glob Antimicrob Resist 2024:S2213-7165(24)00167-X. [PMID: 39278463 DOI: 10.1016/j.jgar.2024.08.012] [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: 05/03/2024] [Revised: 07/30/2024] [Accepted: 08/21/2024] [Indexed: 09/18/2024] Open
Abstract
OBJECTIVES Clinical microbiologists require easy-to-use open access tools with graphical interfaces to perform bacterial whole-genome sequencing (WGS) in routine practice. This study aimed to build a bioinformatics pipeline on the open-source Galaxy platform, facilitating comprehensive and reproducible analysis of bacterial WGS data in a few steps. We then used it to characterize our local epidemiology of ESBL-producing Enterobacterales isolated from patients with bacteremia. METHODS We built a bioinformatics pipeline consisting of the following sequential tools: Fastp (input data trimming); FastQC (read quality control); SPAdes (genome assembly); Quast (quality control of genome assembly); Prokka (gene annotation); Staramr (ResFinder database) and ABRicate (CARD database) for antimicrobial resistance (AMR) gene screening and molecular strain typing. Paired-end short read WGS data from all ESBL-producing Enterobacterales strains isolated from patients with bacteremia over one year were analyzed. RESULTS The Galaxy platform does not require command line tools. The bioinformatics pipeline was constructed within one hour. It only required uploading fastq files and facilitated systematization of the de novo assembly of genomes, MLST typing, and AMR gene screening in one step. Among the 66 ESBL-producing strains analyzed, the two most frequent ESBL genes were blaCTX-M-15 (62.1 %) and blaCTX-M-27 (13.6 %). CONCLUSIONS The open-access Galaxy platform provides a graphical interface and easy-to-use tools suitable for routine use in clinical microbiology laboratories without bioinformatics specialists. We believe that this platform will facilitate fast and low-cost analysis of bacterial WGS data, especially in resource-limited settings.
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Affiliation(s)
- Aimé Berwa
- Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France; Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, CEA, IBS, 38000 Grenoble, France
| | - Yvan Caspar
- Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France; Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, CEA, IBS, 38000 Grenoble, France.
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Opitz-Ríos C, Burgos-Pacheco A, Paredes-Cárcamo F, Campanini-Salinas J, Medina DA. Metagenomics Insight into Veterinary and Zoonotic Pathogens Identified in Urban Wetlands of Los Lagos, Chile. Pathogens 2024; 13:788. [PMID: 39338979 PMCID: PMC11434653 DOI: 10.3390/pathogens13090788] [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: 07/19/2024] [Revised: 08/25/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Wetlands are ecosystems that are essential to ecological balance and biodiversity; nevertheless, human activity is a constant threat to them. Excess nutrients are caused by intensive livestock and agricultural operations, pollution, and population growth, which in turn leads to uncontrolled microbiological development. This impairment in water quality can constitute a risk to animal, human, and environmental health. To thoroughly characterize the microbial communities, shotgun metagenomics was used to characterize the taxonomic and functional pattern of microorganisms that inhabit urban wetlands in the Los Lagos Region of Chile. The main objective was to identify microorganisms of veterinary relevance, assess their potential antibiotic resistance, and characterize the main virulence mechanism. As expected, a high diversity of microorganisms was identified, including bacteria described as animal or human pathogens, such as Pasteurella multocida, Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli. Also, a diverse repertory of antimicrobial-resistant genes (ARGs) was detected in metagenomic assembled sequences and inside the sequence of mobile genetic elements, genes that confer mainly resistance to beta-lactams, consistent with the families of antibiotics most used in Chile. In addition, a diverse collection of virulence mechanisms was also identified. Given the significance of the relationship between environmental, animal, and human health-a concept known as One Health-there is a need to establish molecular surveillance programs that monitor the environmental biohazard elements using molecular tools. This work is the first report of the presence of these harmful biological elements in urban wetlands subjected to anthropogenic pressure, located in the south of Chile.
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Affiliation(s)
- Catherine Opitz-Ríos
- Laboratorio Institucional, Universidad San Sebastián, Puerto Montt 5501842, Chile;
| | - Alvaro Burgos-Pacheco
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Naturaleza, Universidad San Sebastián, Puerto Montt 5501842, Chile; (A.B.-P.); (F.P.-C.)
| | - Francisca Paredes-Cárcamo
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Naturaleza, Universidad San Sebastián, Puerto Montt 5501842, Chile; (A.B.-P.); (F.P.-C.)
| | | | - Daniel A. Medina
- Laboratorio Institucional, Universidad San Sebastián, Puerto Montt 5501842, Chile;
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Naturaleza, Universidad San Sebastián, Puerto Montt 5501842, Chile; (A.B.-P.); (F.P.-C.)
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29
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Lopes J, de Lencastre H, Conceição T. Genomic analysis of Enterococcus faecium from non-clinical settings: antimicrobial resistance, virulence, and clonal population in livestock and the urban environment. Front Microbiol 2024; 15:1466990. [PMID: 39323892 PMCID: PMC11422121 DOI: 10.3389/fmicb.2024.1466990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 08/20/2024] [Indexed: 09/27/2024] Open
Abstract
Introduction Enterococci are commensals of the gastrointestinal tract of humans and animals that evolved into opportunistic pathogens with high antimicrobial resistance and virulence. Multidrug-resistant Enterococcus is a major cause of hospital-acquired infections worldwide. For this reason, the characterization of non-clinical reservoirs of Enterococci and their epidemiological link to resistant hospital isolates is crucial for controlling their spread. Methods A total of 295 samples collected from livestock (pigs and cows, n = 135) and environment (public buses, passengers hands, and urban environments, n = 160) were screened for Enterococcus spp. E. faecium antimicrobial resistance profiles, virulence potential, and clonal population were further characterized. Results Enterococci were detected in 90.5% (n = 267) of the samples, with a higher prevalence in livestock (100%) than the environment (82.5%, p < 0.0001), but none of the isolates exhibited vancomycin resistance. E. faecalis was the most prevalent species (51.7%), predominantly found in livestock (62.2%), while E. faecium was more common in the environment. Of the 59 E. faecium isolates, 78% showed resistance to ≥3 antibiotic classes and contained associated resistance genes, namely tetracyclines (tetM and tetL), beta-lactams (mutations in pbp5), and high-level resistance to aminoglycosides (ant(6)-Ia and aac(6')-aph(2″)). A wide array of virulence factors was detected among E. faecium, associated with adherence, biofilm formation, and adaptation to host response, while hospital-associated virulence markers, such as IS16, were less frequent, probably due to the non-clinical nature of the isolates. Clonal population analysis revealed a diverse E. faecium population. Although no direct epidemiological link could be traced between our isolates and specific clinical isolates, infection-associated genetic backgrounds were identified in non-clinical isolates: one isolate from pigs belonged to CC17 (ST32), while four isolates belonged to CC94, including one recovered from pigs (ST296), one from cows (ST2206), one from the urban environment (ST1205), and other from buses (ST800). Discussion This study underscores a high prevalence of clinically relevant Enterococcus species among healthy livestock and the environment. Despite the absence of vancomycin resistance and limited hospital infection-associated clonal lineages, the presence of E. faecium with significant virulence potential and resistance to critical antibiotics in human and veterinary medicine highlights the need for continuing surveillance of non-clinical reservoirs.
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Affiliation(s)
- Jéssica Lopes
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, United States
| | - Teresa Conceição
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
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30
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Nomoto R, Nakanishi N, Komatsu S, Matsui M, Suzuki S. Complete genome sequences of Escherichia coli KA0011 clinical isolate used as a quality control strain of carbapenem susceptibility testing in Japan. Microbiol Resour Announc 2024; 13:e0015524. [PMID: 39162449 PMCID: PMC11384744 DOI: 10.1128/mra.00155-24] [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: 02/15/2024] [Accepted: 07/26/2024] [Indexed: 08/21/2024] Open
Abstract
Escherichia coli KA0011 had stable minimum inhibitory concentration values around the breakpoint range of meropenem and imipenem, making it suitable for use as a quality control strain for antimicrobial susceptibility testing. Here, we report the complete genomic sequence of KA0011.
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Affiliation(s)
- Ryohei Nomoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Noriko Nakanishi
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Shoko Komatsu
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Mari Matsui
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satowa Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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Mourkas E, Valdebenito JO, Marsh H, Hitchings MD, Cooper KK, Parker CT, Székely T, Johansson H, Ellström P, Pascoe B, Waldenström J, Sheppard SK. Proximity to humans is associated with antimicrobial-resistant enteric pathogens in wild bird microbiomes. Curr Biol 2024; 34:3955-3965.e4. [PMID: 39142288 DOI: 10.1016/j.cub.2024.07.059] [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: 02/13/2024] [Revised: 05/21/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024]
Abstract
Humans are radically altering global ecology, and one of the most apparent human-induced effects is urbanization, where high-density human habitats disrupt long-established ecotones. Changes to these transitional areas between organisms, especially enhanced contact among humans and wild animals, provide new opportunities for the spread of zoonotic pathogens. This poses a serious threat to global public health, but little is known about how habitat disruption impacts cross-species pathogen spread. Here, we investigated variation in the zoonotic enteric pathogen Campylobacter jejuni. The ubiquity of C. jejuni in wild bird gut microbiomes makes it an ideal organism for understanding how host behavior and ecology influence pathogen transition and spread. We analyzed 700 C. jejuni isolate genomes from 30 bird species in eight countries using a scalable generalized linear model approach. Comparing multiple behavioral and ecological traits showed that proximity to human habitation promotes lineage diversity and is associated with antimicrobial-resistant (AMR) strains in natural populations. Specifically, wild birds from urban areas harbored up to three times more C. jejuni genotypes and AMR genes. This study provides novel methodology and much-needed quantitative evidence linking urbanization to gene pool spread and zoonoses.
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Affiliation(s)
- Evangelos Mourkas
- Ineos Oxford Institute, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Zoonosis Science Centre, Department of Medical Sciences, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - José O Valdebenito
- Bird Ecology Lab, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Independencia 631, 5110566 Valdivia, Chile; Centro de Humedales Río Cruces (CEHUM), Universidad Austral de Chile, Camino Cabo Blanco Alto s/n, 5090000 Valdivia, Chile; HUN-REN-DE Reproductive Strategies Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, 8320000 Santiago, Chile
| | - Hannah Marsh
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Matthew D Hitchings
- Institute of Life Science, Swansea University Medical School, Swansea University, Singleton Park, SA2 8PP Swansea, Wales
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA
| | - Craig T Parker
- Produce Safety and Microbiology Unit, Western Region Research Center, USDA, Agricultural Research Service, Albany, CA 94710, USA
| | - Tamás Székely
- HUN-REN-DE Reproductive Strategies Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Håkan Johansson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Stuvaregatan 2, 392 31 Kalmar, Sweden
| | - Patrik Ellström
- Zoonosis Science Centre, Department of Medical Sciences, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Ben Pascoe
- Ineos Oxford Institute, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Stuvaregatan 2, 392 31 Kalmar, Sweden
| | - Samuel K Sheppard
- Ineos Oxford Institute, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
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32
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Pascoe B, Futcher G, Pensar J, Bayliss SC, Mourkas E, Calland JK, Hitchings MD, Joseph LA, Lane CG, Greenlee T, Arning N, Wilson DJ, Jolley KA, Corander J, Maiden MCJ, Parker CT, Cooper KK, Rose EB, Hiett K, Bruce BB, Sheppard SK. Machine learning to attribute the source of Campylobacter infections in the United States: A retrospective analysis of national surveillance data. J Infect 2024; 89:106265. [PMID: 39245152 DOI: 10.1016/j.jinf.2024.106265] [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: 01/26/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/10/2024]
Abstract
OBJECTIVES Integrating pathogen genomic surveillance with bioinformatics can enhance public health responses by identifying risk and guiding interventions. This study focusses on the two predominant Campylobacter species, which are commonly found in the gut of birds and mammals and often infect humans via contaminated food. Rising incidence and antimicrobial resistance (AMR) are a global concern, and there is an urgent need to quantify the main routes to human infection. METHODS During routine US national surveillance (2009-2019), 8856 Campylobacter genomes from human infections and 16,703 from possible sources were sequenced. Using machine learning and probabilistic models, we target genetic variation associated with host adaptation to attribute the source of human infections and estimate the importance of different disease reservoirs. RESULTS Poultry was identified as the primary source of human infections, responsible for an estimated 68% of cases, followed by cattle (28%), and only a small contribution from wild birds (3%) and pork sources (1%). There was also evidence of an increase in multidrug resistance, particularly among isolates attributed to chickens. CONCLUSIONS National surveillance and source attribution can guide policy, and our study suggests that interventions targeting poultry will yield the greatest reductions in campylobacteriosis and spread of AMR in the US. DATA AVAILABILITY All sequence reads were uploaded and shared on NCBI's Sequence Read Archive (SRA) associated with BioProjects; PRJNA239251 (CDC / PulseNet surveillance), PRJNA287430 (FSIS surveillance), PRJNA292668 & PRJNA292664 (NARMS) and PRJNA258022 (FDA surveillance). Publicly available genomes, including reference genomes and isolates sampled worldwide from wild birds are associated with BioProject accessions: PRJNA176480, PRJNA177352, PRJNA342755, PRJNA345429, PRJNA312235, PRJNA415188, PRJNA524300, PRJNA528879, PRJNA529798, PRJNA575343, PRJNA524315 and PRJNA689604. Contiguous assemblies of all genome sequences compared are available at Mendeley data (assembled C. coli genomes doi: 10.17632/gxswjvxyh3.1; assembled C. jejuni genomes doi: 10.17632/6ngsz3dtbd.1) and individual project and accession numbers can be found in Supplementary tables S1 and S2, which also includes pubMLST identifiers for assembled genomes. Figshare (10.6084/m9.figshare.20279928). Interactive phylogenies are hosted on microreact separately for C. jejuni (https://microreact.org/project/pascoe-us-cjejuni) and C. coli (https://microreact.org/project/pascoe-us-ccoli).
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Affiliation(s)
- Ben Pascoe
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Georgina Futcher
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Johan Pensar
- Department of Mathematics, University of Oslo, Oslo, Norway
| | - Sion C Bayliss
- Bristol Veterinary School, University of Bristol, Langford, Bristol, United Kingdom
| | - Evangelos Mourkas
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom; Zoonosis Science Centre, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jessica K Calland
- Oslo University Hospital, Oslo Centre for Biostatistics and Epidemiology, Oslo, Norway
| | - Matthew D Hitchings
- Swansea University Medical School, Swansea University, Swansea, United Kingdom
| | - Lavin A Joseph
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Charlotte G Lane
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tiffany Greenlee
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Nicolas Arning
- Big Data Institute, Oxford Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, United Kingdom
| | - Daniel J Wilson
- Big Data Institute, Oxford Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, United Kingdom; Department for Continuing Education, University of Oxford, United Kingdom
| | - Keith A Jolley
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Jukka Corander
- Oslo University Hospital, Oslo Centre for Biostatistics and Epidemiology, Oslo, Norway; Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland; Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Craig T Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, CA, USA
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Erica B Rose
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kelli Hiett
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, USA
| | - Beau B Bruce
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Samuel K Sheppard
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom.
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Lee KY, Schlesener CL, Aly SS, Huang BC, Li X, Atwill ER, Weimer BC. Whole genome sequence analysis reveals high genomic diversity and potential host-driven adaptations among multidrug-resistant Escherichia coli from pre-weaned dairy calves. Front Microbiol 2024; 15:1420300. [PMID: 39296303 PMCID: PMC11409426 DOI: 10.3389/fmicb.2024.1420300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 08/16/2024] [Indexed: 09/21/2024] Open
Abstract
Food-producing animals such as dairy cattle are potential reservoirs of antimicrobial resistance (AMR), with multidrug-resistant (MDR) organisms such as Escherichia coli observed in higher frequency in young calves compared to older cattle. In this study, we characterized the genomes of enteric MDR E. coli from pre-weaned dairy calves with and without diarrhea and evaluated the influence of host-level factors on genomic composition. Whole genome sequence comparative analysis of E. coli (n = 43) revealed substantial genomic diversity that primarily clustered by sequence type and was minimally driven by calf diarrheal disease status (healthy, diarrheic, or recovered), antimicrobial exposure, and dietary zinc supplementation. Diverse AMR genes (ARGs)-including extended-spectrum beta-lactamase genes and quinolone resistance determinants-were identified (n = 40), with unique sets of ARGs co-occurring in gene clusters with large AMR plasmids IncA/C2 and IncFIB(AP001918). Zinc supplementation was not significantly associated with the selection of individual ARGs in E. coli, however analysis of ARG and metal resistance gene pairs identified positive associations between certain aminoglycoside, beta-lactam, sulfonamide, and trimethoprim ARGs with acid, tellurium and mercury resistance genes. Although E. coli in this study lacked the typical virulence factors of diarrheagenic strains, virulence genes overlapping with those in major pathotypes were identified. Among the 103 virulence genes detected, the highest abundance and diversity of genes corresponded to iron acquisition (siderophores and heme uptake). Our findings indicate that the host-level factors evaluated in this study were not key drivers of genomic variability, but that certain accessory genes in enteric MDR E. coli may be enriched. Collectively, this work provides insight into the genomic diversity and host-microbe interface of MDR E. coli from pre-weaned dairy calves.
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Affiliation(s)
- Katie Y Lee
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Cory L Schlesener
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Sharif S Aly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
| | - Bihua C Huang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Xunde Li
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Edward R Atwill
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Bart C Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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Magome TG, Ochai SO, Hassim A, Bezuidenhout CC, van Heerden H, Lekota KE. A genome-based investigation of the Priestia species isolated from anthrax endemic regions in Kruger National Park. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105649. [PMID: 39059732 DOI: 10.1016/j.meegid.2024.105649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 07/21/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024]
Abstract
Priestia is a genus that was renamed from the genus Bacillus based on the conserved signature indels (CSIs) in protein sequences that separate Priestia species from Bacillus, with the latter only including species closely related to B. subtilis and B. cereus. Diagnosis of anthrax, a zoonotic disease, is implicated by tripartite anthrax virulence genes (lef, pagA, and cya) and poly-γ-D-glutamic acid capsular genes cap-ABCDE of Bacillus anthracis. Due to the amplification of anthrax virulence genes in Priestia isolates, the search for homologous anthrax virulence genes within the Priestia genomes (n = 9) isolated from animal blood smears was embarked upon through whole genome sequencing. In silico taxonomic identification of the isolates was conducted using genome taxonomy database (GTDB), average nucleotide identity (ANI), and multi-locus sequence typing (MLST), which identified the genomes as P. aryabhattai (n = 5), P. endophytica (n = 2) and P. megaterium (n = 2). A pan-genome analysis was further conducted on the Priestia genomes, including the screening of virulence, antibiotic resistance genes and mobile genetic elements on the sequenced genomes. The oligoribonuclease NrnB protein sequences showed that Priestia spp. possess a unique CSI that is absent in other Bacillus species. Furthermore, the CSI in P. endophytica is unique from other Priestia spp. Pan-genomic analysis indicates that P. endophytica clusters separately from P. aryabhattai and P. megaterium. In silico BLASTn genome analysis using the SYBR primers, Taqman probes and primers that target the chromosomal marker (Ba-1), protective antigen (pagA), and lethal factor (lef) on B. anthracis, showed partial binding to Priestia regions encoding for hypothetical proteins, pyridoxine biosynthesis, hydrolase, and inhibitory proteins. The antibiotic resistance genes (ARG) profile of Priestia spp. showed that the genomes contained no more than two ARGs. This included genes conferring resistance to rifamycin and fosfomycin on P. endophytica, as well as clindamycin on P. aryabhattai and P. megaterium. Priestia genomes lacked B. anthracis plasmids and consisted of plasmid replicon types with unknown functions. Furthermore, the amplification of Priestia strains may result in false positives when qPCR is used to detect the virulence genes of B. anthracis in soil, blood smears, and/or environmental samples.
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Affiliation(s)
- Thuto Gomolemo Magome
- Unit for Environmental Sciences and Management, Microbiology, North-West University, Potchefstroom, South Africa.
| | - Sunday Ochonu Ochai
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa; International Centre for Antimicrobial Resistance Solutions, Copenhagen S, 2300, Denmark; Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ayesha Hassim
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | | | - Henriette van Heerden
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Kgaugelo Edward Lekota
- Unit for Environmental Sciences and Management, Microbiology, North-West University, Potchefstroom, South Africa
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Isogai M, Kawamura K, Yagi T, Kayama S, Sugai M, Doi Y, Suzuki M. Evaluation of Klebsiella pneumoniae pathogenicity through holistic gene content analysis. Microb Genom 2024; 10. [PMID: 39298254 DOI: 10.1099/mgen.0.001295] [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: 09/21/2024] Open
Abstract
Klebsiella pneumoniae is a Gram-negative bacterium that causes both community- and healthcare-associated infections. Although various virulence factors and highly pathogenic phenotypes have been reported, the pathogenicity of K. pneumoniae is still not fully understood. In this study, we utilized whole-genome sequencing data of 168 clinical K. pneumoniae strains to assess pathogenicity. This work was based on the concept that the genetic composition of individual genomes (referred to as holistic gene content) of the strains may contribute to their pathogenicity. Holistic gene content analysis revealed two distinct groups of K. pneumoniae strains ('major group' and 'minor group'). The minor group included strains with known highly pathogenic clones (ST23, ST375, ST65 and ST86). The minor group had higher rates of capsular genotype K1 and presence of nine specific virulence genes (rmpA, iucA, iutA, irp2, fyuA, ybtS, iroN, allS and clbA) compared to the major group. Pathogenicity was assessed using Galleria mellonella larvae. Infection experiments revealed lower survival rates of larvae infected with strains from the minor group, indicating higher virulence. In addition, the minor group had a higher string test positivity rate than the major group. Holistic gene content analysis predicted possession of virulence genes, string test positivity and pathogenicity as observed in the G. mellonella infection model. Moreover, the findings suggested the presence of as yet unrecognized genomic elements that are either involved in the acquisition of virulence genes or associated with pathogenicity.
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Affiliation(s)
- Miyu Isogai
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Kumiko Kawamura
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shizuo Kayama
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Yohei Doi
- Department of Microbiology, Fujita Health University School of Medicine, Aichi, Japan
- Center for Infectious Disease Research, Fujita Health University, Toyoake, Aichi, Japan
- Department of Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
- Center for Innovative Antimicrobial Therapy, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Masahiro Suzuki
- Department of Microbiology, Fujita Health University School of Medicine, Aichi, Japan
- Center for Infectious Disease Research, Fujita Health University, Toyoake, Aichi, Japan
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Tang C, Shen S, Yang W, Shi Q, Ding L, Han R, Yin D, Guo Y, Zhu D, Hu F. Complex evolutionary trajectories in vivo of two novel KPC variants conferring ceftazidime-avibactam resistance. Int J Antimicrob Agents 2024; 64:107265. [PMID: 38964622 DOI: 10.1016/j.ijantimicag.2024.107265] [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: 01/26/2024] [Revised: 05/08/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024]
Abstract
More and more ceftazidime-avibactam-resistant KPC-producing Klebsiella pneumoniae have been reported with its widespread use, and the detection rate of KPC variants has increased dramatically. However, the evolutionary mechanism and fitness effects during KPC mutation remained unknown. Here, we report the complex in vivo evolutionary trajectories of two novel KPC variants, KPC-155 (L169P/GT242A) and KPC-185 (D179Y/GT242A), from K. pneumoniae in the same patient. The novel variants were shown to confer ceftazidime-avibactam resistance but restore carbapenem susceptibility based on the results of plasmid transformation assays, cloning experiments, and enzyme kinetic measurements. In vitro, competition experiments highlighted the adaptive advantage conferred by strains carrying these KPC variants, which could lead to the rapid spread of these ceftazidime-avibactam-resistant strains. The growth curve indicated that blaKPC-185 had better growth conditions at lower avibactam concentration compared to blaKPC-155, which was consistent with ceftazidime-avibactam use in vivo. In addition, replicative transposition of the IS26-flanked translocatable unit (IS26-ISKpn6-blaKPC-ISKpn27-IS26) also contributes to the blaKPC amplification and formation of two copies (blaKPC-2 and blaKPC-185), conferring both carbapenem and ceftazidime-avibactam resistance. However, strains with double copies showed reduced competitive advantage and configuration stability. The comparative plasmid analysis of IS26 group (IS26-blaKPC-IS26) and Tn1721 group (Tn1721-blaKPC-IS26) revealed that IS26-insertion could influence the distribution of resistance genes and ability of self-conjugation. The dynamic changes in blaKPC configuration highlight the need for consistent monitoring including antimicrobial susceptibility testing and determination of blaKPC subtypes - during clinical treatment, especially when ceftazidime-avibactam is administered.
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Affiliation(s)
- Chengkang Tang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Siquan Shen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Weiwei Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Qingyu Shi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Li Ding
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Renru Han
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Dandan Yin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Yan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Demei Zhu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China.
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Tian C, Di L, Dong S, Tian X, Huang D, Zhao Y, Chen J, Xia D, Wang S. Whole genome sequencing and genomic characteristics analysis of carbapenem-resistant Acinetobacter baumannii clinical isolates in two hospitals in China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105642. [PMID: 39013496 DOI: 10.1016/j.meegid.2024.105642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/18/2024]
Abstract
Nosocomial outbreaks caused by carbapenem-resistant Acinetobacter baumannii (CRAB) strains are rapidly emerging worldwide and are cause for concern. Herein, we aimed to describe the genomic characteristics of CRAB strains isolated from two hospitals in China in 2023. The A. baumannii isolates were mainly collected from the ICU and isolated from the sputum (71.43%, 15/21), followed by urine (14.29%, 3/21). Twenty-one A. baumannii strains possessed a multidrug-resistant (MDR) profile, and whole-genome sequencing showed that they all carried blaOXA-23. Based on the Pasteur multilocus sequence typing (MLST) scheme, all strains were typed into a sequence type 2 (ST2). Based on the Oxford MLST scheme, six strains belonged to ST540, three of which were ST208, and four strains were assigned to ST784. Kaptive showed most of the strains (38.10%, 8/21) contained KL93. As for the lipoolygosaccharide (OC locus) type, OCL1c and OCL1d were identified, accounting for 33.33% (7/21) and 66.67% (14/21), respectively. Based on the BacWGSTdb server, we found that the strains belonging to ST540 and ST784 were all collected from China. However, the ST938 strains were isolated from Malaysia and Thailand. Comparative genomics analysis showed that the AB10 strain had a closed relationship with SXAB10-SXAB13 strains, suggesting the transmission happened in these two hospitals and other hospital in China. In addition, the 4300STDY7045869 strain, which was collected from Thailand, possessed near genetic relationship with our isolates in this study, suggesting the possible spread among various countries. Additionally, 3-237 single nucleotide polymorphisms were observed among these strains. In conclusion, this study conducted a genome-based study for A. baumannii strains collected from two hospitals in China and revealed their epidemiological and molecular features. Clone spreading occurred in these two hospitals. Hence, there is an urgent need for increased surveillance in hospitals and other clinical settings to prevent and control CRAB spreading.
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Affiliation(s)
- Chongmei Tian
- Department of Pharmacy, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, Zhejiang 312000, China
| | - Lingfang Di
- Department of Clinical Laboratory, Tongxiang First People's Hospital, Tongxiang, Zhejiang 314500, China
| | - Su Dong
- Department of Clinical Laboratory, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, Zhejiang 312000, China
| | - Xuebin Tian
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Delian Huang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yaping Zhao
- Department of Pharmacy, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, Zhejiang 312000, China
| | - Jingbai Chen
- Department of Pharmacy, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, Zhejiang 312000, China
| | - Daozong Xia
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Siwei Wang
- Panvascular Diseases Research Center, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China.
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He X, He J, Tang J, Huang X, Yu Y, Hua X. Genetic characterization of plasmid-borne bla OXA-58 and bla OXA-72 in Acinetobacter pittii in Shaanxi, China. J Glob Antimicrob Resist 2024; 38:167-172. [PMID: 38768708 DOI: 10.1016/j.jgar.2024.05.007] [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: 12/14/2023] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/22/2024] Open
Abstract
OBJECTIVES Acinetobacter pittii has emerged as an opportunistic nosocomial pathogen associated with hospital-acquired infections. The purpose of this study was to investigate the genetic structures of plasmids carrying carbapenemase genes blaOXA-58 and blaOXA-72 in A. pittii strains AR3676 and AR3651 isolated from patients. METHODS Antimicrobial susceptibility testing was performed using broth microdilution. Whole-genome sequencing and bioinformatics analysis were performed to characterize the genome of A. pittii AR3676 and AR3651. Conjugation experiments were conducted to evaluate plasmid transferability. Phylogenetic and comparative genomic analysis were performed to explore the characteristics of carbapenem-resistant A. pittii isolates worldwide. RESULTS The AR3676 strain showed resistance to imipenem. The 19 700-bp plasmid pAR3676-OXA-58 harboured blaOXA-58 with genetic contexts consisting of a truncated ISAba3-like-blaOXA58-ISAba3. Additionally, the AR3651 strain showed resistance to imipenem and meropenem. The AR3651 genome comprised one 9,837-bp RepA_AB plasmid pAR3651-OXA-72 harbouring blaOXA-72. This blaOXA-72 was flanked by XerC/XerD recombination sites. The conjugation of plasmids pAR3676-OXA-58 and pAR3651-OXA-72 from A. pittii to Acinetobacter baumannii ATCC 17978RIFR failed three independent times. Phylogenetic analysis of A. pittii strains AR3676, AR3651, and a further 504 A. pittii strains collected between 1966 and 2022 from various geographic localities revealed genetic diversity with a heterogeneous distribution of carbapenemase genes. CONCLUSIONS A. pittii strains with a plasmid carrying blaOXA-58 or blaOXA-72 may serve as an important reservoir of carbapenemase genes. Carbapenemase genes on a single plasmid may facilitate their dissemination and persistence. Additionally, pdif sites and mobile elements play an important role in the mobilization of resistance genes and plasmid evolution.
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Affiliation(s)
- Xiaoliang He
- Department of Clinical Laboratory, Hanzhong Central Hospital, Hanzhong, People's Republic of China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People's Republic of China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Jintao He
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People's Republic of China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Jin Tang
- Department of Clinical Laboratory, Hanzhong Central Hospital, Hanzhong, People's Republic of China
| | - Xiaoxia Huang
- Department of Clinical Laboratory, Hanzhong Central Hospital, Hanzhong, People's Republic of China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People's Republic of China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People's Republic of China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China.
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Han K, Yue J, Li J, Zhang J, Lin J, Zhuang Q, Li N, Li S, Rong C, Hua M, Liu Y, Yang D, Gu C, Chen L, Zeng H, Chen C. Emergence of mcr-4.3 genes in a novel Shewanella specie isolated from the Arctic environment. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105636. [PMID: 38972619 DOI: 10.1016/j.meegid.2024.105636] [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: 03/22/2024] [Revised: 06/28/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
Mobile colistin resistance (mcr) genes are pivotal contributors to last-line of antimicrobial resistance in human infections. Shewanella, historically recognized as a natural environmental bacterium with metal reduction capabilities, recently has been observed in clinical settings. However, limited knowledge has been explored on genetic differences between strains from non-clinical and clinical strains. In this study, we conducted the whole genome sequencing on six Arctic strains, illustrated the phylogenetic relationships on published 393 Shewanella strains that categorized the genus into four lineages (L1 to L4). Over 86.4% of clinical strain group (CG) strains belonged to L1 and L4, carrying mcr-4 genes and a complete metal-reduction pathways gene cluster. Remarkably, a novel Arctic Shewanella strain in L3, exhibits similar genetic characteristics with CG strains that carried both mcr-4 genes and a complete metal reduction pathway gene cluster. It raised concerns about the transmission ability from environment to clinic setting causing in the potential infections, and emphasized the need for monitoring the emerging strains with human infections.
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Affiliation(s)
- Kai Han
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jinglin Yue
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jiarui Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jiuming Zhang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Jing Lin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Qinghui Zhuang
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Na Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Sha Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chengbo Rong
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Mingxi Hua
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yuwei Liu
- Emergency Department, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Duo Yang
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chaoyang Gu
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Liang Chen
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hui Zeng
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chen Chen
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
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Liu Y, Wang Q, Qi T, Zhang M, Chen R, Si Z, Li J, Jin Y, Xu Q, Li P, Hao Y. Molecular Epidemiology of mcr-1-Positive Polymyxin B-Resistant Escherichia coli Producing Extended-Spectrum β-Lactamase (ESBL) in a Tertiary Hospital in Shandong, China. Pol J Microbiol 2024; 73:363-375. [PMID: 39268958 PMCID: PMC11395425 DOI: 10.33073/pjm-2024-032] [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: 05/15/2024] [Accepted: 07/23/2024] [Indexed: 09/15/2024] Open
Abstract
Escherichia coli, a rod-shaped Gram-negative bacterium, is a significant causative agent of severe clinical bacterial infections. This study aimed to analyze the epidemiology of extended-spectrum β-lactamase (ESBL)-producing mcr-1 -positive E. coli in Shandong, China. We collected 668 non-duplicate ESBL-producing E. coli strains from clinical samples at Shandong Provincial Hospital between January and December 2018, and estimated their minimum inhibitory concentrations (MICs) using a VITEK® 2 compact system and broth microdilution. Next-generation sequencing and bioinformatic analyses identified the mcr-1 gene and other resistance genes in the polymyxin B-resistant strains. The conjugation experiment assessed the horizontal transfer capacity of the mcr-1 gene. Of the strains collected, 24 polymyxin B-resistant strains were isolated with a positivity rate of 3.59% and among the 668 strains, 19 clinical strains carried the mobile colistin resistance gene mcr-1, with a positivity rate of approximately 2.8%. All 19 clinical strains were resistant to ampicillin, cefazolin, ceftriaxone, ciprofloxacin, levofloxacin, and polymyxin B. Seventeen strains successfully transferred the mcr-1 gene into E. coli J53. All transconjugants were resistant to polymyxin B, and carried the drug resistance gene mcr-1. The 19 clinical strains had 14 sequence types (STs), with ST155 (n = 4) being the most common. The whole-genome sequencing results of pECO-POL-29_mcr1 revealed that no ISApl1 insertion sequences were found on either side of the mcr-1 gene. Our study uncovered the molecular epidemiology of mcr-1-carrying ESBL-producing E. coli in the region and suggested horizontal transmission mediated by plasmids as the main mode of mcr-1 transmission.
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Affiliation(s)
- Yue Liu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Qian Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ting Qi
- Department of Clinical Laboratory, Jinan Gangcheng District People’s Hospital, Jinan, China
| | - Meng Zhang
- Department of Clinical Laboratory, Liaocheng Second People’s Hospital, Liaocheng, China
| | - Ran Chen
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zaifeng Si
- Department of Clinical Laboratory, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jinmei Li
- Department of Clinical Laboratory, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Clinical Laboratory, Jinan Seventh People’s Hospital, Jinan, China
| | - Yan Jin
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Qingbing Xu
- Central Laboratory of Liaocheng People’s Hospital, Liaocheng, China
| | - Ping Li
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yingying Hao
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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Moran RA, Behruznia M, Holden E, Garvey MI, McNally A. pQEB1: a hospital outbreak plasmid lineage carrying bla KPC-2. Microb Genom 2024; 10:001291. [PMID: 39222339 PMCID: PMC11368168 DOI: 10.1099/mgen.0.001291] [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: 06/13/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
While conducting genomic surveillance of carbapenemase-producing Enterobacteriaceae (CPE) from patient colonisation and clinical infections at Birmingham's Queen Elizabeth Hospital (QE), we identified an N-type plasmid lineage, pQEB1, carrying several antibiotic resistance genes, including the carbapenemase gene bla KPC-2. The pQEB1 lineage is concerning due to its conferral of multidrug resistance, its host range and apparent transmissibility, and its potential for acquiring further resistance genes. Representatives of pQEB1 were found in three sequence types (STs) of Citrobacter freundii, two STs of Enterobacter cloacae, and three species of Klebsiella. Hosts of pQEB1 were isolated from 11 different patients who stayed in various wards throughout the hospital complex over a 13 month period from January 2023 to February 2024. At present, the only representatives of the pQEB1 lineage in GenBank were carried by an Enterobacter hormaechei isolated from a blood sample at the QE in 2016 and a Klebsiella pneumoniae isolated from a urine sample at University Hospitals Coventry and Warwickshire (UHCW) in May 2023. The UHCW patient had been treated at the QE. Long-read whole-genome sequencing was performed on Oxford Nanopore R10.4.1 flow cells, facilitating comparison of complete plasmid sequences. We identified structural variants of pQEB1 and defined the molecular events responsible for them. These have included IS26-mediated inversions and acquisitions of multiple insertion sequences and transposons, including carriers of mercury or arsenic resistance genes. We found that a particular inversion variant of pQEB1 was strongly associated with the QE Liver speciality after appearing in November 2023, but was found in different specialities and wards in January/February 2024. That variant has so far been seen in five different bacterial hosts from six patients, consistent with recent and ongoing inter-host and inter-patient transmission of pQEB1 in this hospital setting.
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Affiliation(s)
- Robert A. Moran
- Institute of Microbiology and Infection, School of Medical and Dental Sciences, The University of Birmingham, Edgbaston B15 2TT, UK
| | - Mahboobeh Behruznia
- Institute of Microbiology and Infection, School of Medical and Dental Sciences, The University of Birmingham, Edgbaston B15 2TT, UK
| | - Elisabeth Holden
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Edgbaston, B15 2WB, UK
| | - Mark I. Garvey
- Institute of Microbiology and Infection, School of Medical and Dental Sciences, The University of Birmingham, Edgbaston B15 2TT, UK
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Edgbaston, B15 2WB, UK
| | - Alan McNally
- Institute of Microbiology and Infection, School of Medical and Dental Sciences, The University of Birmingham, Edgbaston B15 2TT, UK
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Goel A, Halami PM. Safety assessment of probiotic Lactiplantibacillus plantarum MCC5231 and its persistence in gastrointestinal tract. Microb Pathog 2024; 194:106824. [PMID: 39067492 DOI: 10.1016/j.micpath.2024.106824] [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: 04/18/2024] [Revised: 07/21/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
Probiotics are the health beneficial microorganisms and suitable for food industry if found fit for human consumption. In the present study, Lactiplantibacillus plantarum MCC5231, a probiotic bacterium included in vegetable-based beverages, was evaluated for its safety characteristics and gastrointestinal survival using a combined in silico and in vitro approach. The strain was found to be devoid of hemolytic, lecithinase and gelatinase activities. Additionally, it does not consist any transferable antibiotic resistance genes. Further, whole genome sequence analysis revealed the presence of three intact prophages and 14 virulence-associated genes, however, none of them posed a pathogenic threat. Importantly, MCC5231 do not possess any gene associated with toxin production. The strain harbored a CRISPR system, enhancing defense against prophages. Survival assays under simulated gastric and intestinal fluid conditions demonstrated viability rates of 71.4 % and 83.3 %, respectively. Genetic analysis of the mucin binding protein indicated possession of a type II mucin binding domain, suggesting moderate adhesion to intestinal cells. Furthermore, L. plantarum MCC5231 exhibited the ability to produce exopolysaccharides and form biofilms, which may confer additional protection in the gastrointestinal tract. Based on these findings, L. plantarum MCC5231 appears to be a safe probiotic candidate suitable for commercial use in the food industry.
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Affiliation(s)
- Aditi Goel
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, 570020, Karnataka, India.
| | - Prakash M Halami
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, 570020, Karnataka, India.
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Jiang C, Zhao Z, Grossart HP, Ju F, Zhao Y, Gadd GM, Korzeniewska E, Yang Y. Health risk ranking of antibiotic resistance genes in the Yangtze River. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100388. [PMID: 38351955 PMCID: PMC10862502 DOI: 10.1016/j.ese.2024.100388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 02/16/2024]
Abstract
Antibiotic resistance is an escalating global health concern, exacerbated by the pervasive presence of antibiotic resistance genes (ARGs) in natural environments. The Yangtze River, the world's third-longest river, traversing areas with intense human activities, presents a unique ecosystem for studying the impact of these genes on human health. Here, we explored ARGs in the Yangtze River, examining 204 samples from six distinct habitats of approximately 6000 km of the river, including free-living and particle-associated settings, surface and bottom sediments, and surface and bottom bank soils. Employing shotgun sequencing, we generated an average of 13.69 Gb reads per sample. Our findings revealed a significantly higher abundance and diversity of ARGs in water-borne bacteria compared to other habitats. A notable pattern of resistome coalescence was observed within similar habitat types. In addition, we developed a framework for ranking the risk of ARG and a corresponding method for calculating the risk index. Applying them, we identified water-borne bacteria as the highest contributors to health risks, and noted an increase in ARG risks in particle-associated bacteria correlating with heightened anthropogenic activities. Further analysis using a weighted ARG risk index pinpointed the Chengdu-Chongqing and Yangtze River Delta urban agglomerations as regions of elevated health risk. These insights provide a critical new perspective on ARG health risk assessment, highlighting the urgent need for strategies to mitigate the impact of ARGs on human health and to preserve the ecological and economic sustainability of the Yangtze River for future human use.
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Affiliation(s)
- Chunxia Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
| | - Zelong Zhao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Hans-Peter Grossart
- Leibniz-Institute for Freshwater Ecology and Inland Fisheries (IGB), Neuglobsow, 16775, Germany
- Institute for Biochemistry and Biology, Potsdam University, Potsdam, 14469, Germany
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310030, China
| | - Yi Zhao
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum, Beijing, 102249, China
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Olsztyn, 10-720, Poland
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
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Peng J, Xiao R, Wu C, Zheng Z, Deng Y, Chen K, Xiang Y, Xu C, Zou L, Liao M, Zhang J. Characterization of the prevalence of Salmonella in different retail chicken supply modes using genome-wide and machine-learning analyses. Food Res Int 2024; 191:114654. [PMID: 39059904 DOI: 10.1016/j.foodres.2024.114654] [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: 04/22/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/28/2024]
Abstract
Salmonella is a foodborne pathogen that causes salmonellosis, of which retail chicken meat is a major source. However, the prevalence of Salmonella in different retail chicken supply modes and the threat posed to consumers remains unclear. The prevalence, serotype distribution, antibiotic resistance, and genomic characteristics of Salmonella in three supply modes of retail chicken (live poultry, frozen, and chilled) were investigated using whole-genome sequencing (WGS) and machine learning (ML). In this study, 480 retail chicken samples from live poultry, frozen, and chilled supply modes in Guangzhou from 2020 to 2021, as well as 253 Salmonella isolates (total isolation rate = 53.1 %), were collected. The prevalence of isolates in the live poultry mode (67.5 %, 81/120) was statistically higher than in the frozen (50.0 %, 120/240) and chilled (43.3 %, 52/120) (P < 0.05) modes. Serotype identification showed significant differences in the serotype distribution of Salmonella in different supply modes. S. Enteritis (46.7 %) and S. Indiana (14.2 %) were predominant in the frozen mode. S. Agona (23.5 %) and S. Saintpaul (13.6 %) were predominant in live poultry, while S. Enteritis (40.4 %) and S. Kentucky (17.3 %) were predominant in chilled mode. Antibiotic testing showed that frozen mode isolates were more resistant; the multidrug-resistant (MDR) rate of isolates in the frozen mode reached 91.8 %, significantly higher than in the chilled (86.5 %) and live (74.1 %) (P < 0.05) modes. WGS was performed on 155 top serotypes (S. Enteritidis, S. Kentucky, S. Indiana, and S. Agona). The antibiotic resistance gene analysis showed that the abundance and carrying rate of antibiotic resistance genes of Salmonella in the frozen mode (54 types, 16.1 %) were significantly higher than in other modes (live poultry: 36 types, 9.4 %, P < 0.05; chilled: 31 types, 11.6 %). The blaNDM-1 and blaNDM-9 genes encoding carbapenem resistance were found in frozen mode isolates on a complex transposon consisting of TnAS3-IS26. Virulence factors and plasmid replicons were abundant in the studied frozen mode isolates. In addition, single nucleotide polymorphism (SNP) phylogenetic tree results showed that in the frozen supply mode, the S. Enteritidis clonal clade continued to contaminate retail chicken meat and was homologous to S. Enteritidis strains found in farm chicken embryos, slaughterhouse chicken carcasses, and patients from hospitals in China (SNP 0 = 10). Notably, the pan-genome-based ML model showed that characteristic genes in frozen and live poultry isolates differed. The narZ gene was a key characteristic gene in frozen isolates, encoding nitrate reductase, relating to anaerobic bacterial growth. The ydgJ gene is a key characteristic gene in the live mode and encodes an oxidoreductase related to oxidative function in bacteria. The high prevalence of live poultry mode Salmonella and the transmission of frozen mode MDR Salmonella in this study pose serious risks to food safety and public health, emphasizing the importance of improving disinfection and cold storage measures to reduce Salmonella contamination and transmission. In conclusion, the continued surveillance of Salmonella across different supply models and the development of an epidemiological surveillance system based on WGS is necessary.
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Affiliation(s)
- Junhao Peng
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Renhang Xiao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Canji Wu
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zexin Zheng
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yuhui Deng
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Kaifeng Chen
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yuwei Xiang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Chenggang Xu
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Likou Zou
- College of Resource, Sichuan Agricultural University, 611130 Yaan, China
| | - Ming Liao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; School of Resources and Environmental, Zhongkai College of Agricultural Engineering, Guangxin Road No. 388, Baiyun District, Guangzhou 510550, Guangdong, China.
| | - Jianmin Zhang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
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45
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Zhang P, Wang H, Klima C, Yang X. Microbiota in lymph nodes of cattle harvested in a Canadian meat processing plant. Food Res Int 2024; 191:114693. [PMID: 39059949 DOI: 10.1016/j.foodres.2024.114693] [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: 05/26/2024] [Revised: 06/19/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024]
Abstract
Lymph nodes (LN) harboring bacteria, when being incorporated into ground beef, may impact the microbial safety and quality of such products. We tested two main foodborne pathogens Salmonella and Shiga toxin-producing Escherichia coli (STEC) and profiled the microbiota in LNs (n = 160) of cattle harvested at a Canadian abattoir, by conventional plating methods, PCR, and high throughput sequencing. LNs at two anatomical locations, subiliac and popliteal from 80 cattle were included. All cattle had bacteria detected in popliteal and/or subiliac LNs with the maximum bacterial load of 5.4 and 2.8 log10CFU/g in popliteal and subiliac LNs, respectively. Neither Salmonella nor STEC was found in LNs although STEC was detected in a significant percentage of samples from beef hides (50.6 %) by plating and/or PCR. Both 16S rRNA gene amplicon and metagenome sequencing found the predominance of Escherichia (13-34.6 % among bacterial community), Clostridium (12.6-20.6 %) and Streptococcus (9.7-10 %) in popliteal LNs. Metagenomic sequencing was able to identify the predominant taxa at species level with E. coli (13 %), Clostridium perfringens (11.1 %) and Streptococcus uberis (6 %) predominant in LNs. Low prevalence/abundance of Salmonella was found by metagenomic sequencing. In conclusion, the relatively high bacterial load and diversity in LNs may affect the shelf life of ground beef and high relative abundance of E. coli would warrant further monitoring.
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Affiliation(s)
- Peipei Zhang
- Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Hui Wang
- Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Cassidy Klima
- Beef Cattle Research Council, Calgary, Alberta, Canada
| | - Xianqin Yang
- Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada.
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46
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Mitchell TM, Ho T, Salinas L, VanderYacht T, Walas N, Trueba G, Graham JP. Analysis of Antibiotic Resistance Genes (ARGs) across Diverse Bacterial Species in Shrimp Aquaculture. Antibiotics (Basel) 2024; 13:825. [PMID: 39334999 PMCID: PMC11429446 DOI: 10.3390/antibiotics13090825] [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: 05/24/2024] [Revised: 08/09/2024] [Accepted: 08/20/2024] [Indexed: 09/30/2024] Open
Abstract
There is little information available on antibiotic resistance (ABR) within shrimp aquaculture environments. The aim of this study was to investigate the presence of antibiotic resistance genes (ARGs) in shrimp farming operations in Atacames, Ecuador. Water samples (n = 162) and shrimp samples (n = 54) were collected from three shrimp farming operations. Samples were cultured and a subset of isolates that grew in the presence of ceftriaxone, a third-generation cephalosporin, were analyzed using whole-genome sequencing (WGS). Among the sequenced isolates (n = 44), 73% of the isolates contained at least one ARG and the average number of ARGs per isolate was two, with a median of 3.5 ARGs. Antibiotic resistance genes that confer resistance to the β-lactam class of antibiotics were observed in 65% of the sequenced isolates from water (20/31) and 54% of the isolates from shrimp (7/13). We identified 61 different ARGs across the 44 sequenced isolates, which conferred resistance to nine antibiotic classes. Over half of all sequenced isolates (59%, n = 26) carried ARGs that confer resistance to more than one class of antibiotics. ARGs for certain antibiotic classes were more common, including beta-lactams (26 ARGs); aminoglycosides (11 ARGs); chloramphenicol (three ARGs); and trimethoprim (four ARGs). Sequenced isolates consisted of a diverse array of bacterial orders and species, including Escherichia coli (48%), Klebsiella pneumoniae (7%), Aeromonadales (7%), Pseudomonadales (16%), Enterobacter cloacae (2%), and Citrobacter freundii (2%). Many ARGs were shared across diverse species, underscoring the risk of horizontal gene transfer in these environments. This study indicated the widespread presence of extended-spectrum β-lactamase (ESBL) genes in shrimp aquaculture, including blaCTX-M, blaSHV, and blaTEM genes. Increased antibiotic resistance surveillance of shrimp farms and identification of aquaculture operation-level risk factors, such as antibiotic use, will likely be important for mitigating the spread of ARGs of clinical significance.
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Affiliation(s)
- Tilden M Mitchell
- School of Public Health, University of California, Berkeley, CA 94704, USA
| | - Tin Ho
- School of Public Health, University of California, Berkeley, CA 94704, USA
| | - Liseth Salinas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito 170901, Pichincha, Ecuador
| | - Thomas VanderYacht
- School of Public Health, University of California, Berkeley, CA 94704, USA
| | - Nikolina Walas
- School of Public Health, University of California, Berkeley, CA 94704, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito 170901, Pichincha, Ecuador
| | - Jay P Graham
- School of Public Health, University of California, Berkeley, CA 94704, USA
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47
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Becsei Á, Fuschi A, Otani S, Kant R, Weinstein I, Alba P, Stéger J, Visontai D, Brinch C, de Graaf M, Schapendonk CME, Battisti A, De Cesare A, Oliveri C, Troja F, Sironen T, Vapalahti O, Pasquali F, Bányai K, Makó M, Pollner P, Merlotti A, Koopmans M, Csabai I, Remondini D, Aarestrup FM, Munk P. Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance. Nat Commun 2024; 15:7551. [PMID: 39215001 PMCID: PMC11364805 DOI: 10.1038/s41467-024-51957-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve surveillance, we seek to recover sewage genomes and develop a quantification and correlation workflow for these genomes and AMR over time. We use longitudinal sewage sampling in seven treatment plants from five major European cities to explore the utility of catch-all sequencing of these population-level samples. Using metagenomic assembly methods, we recover 2332 metagenome-assembled genomes (MAGs) from prokaryotic species, 1334 of which were previously undescribed. These genomes account for ~69% of sequenced DNA and provide insight into sewage microbial dynamics. Rotterdam (Netherlands) and Copenhagen (Denmark) show strong seasonal microbial community shifts, while Bologna, Rome, (Italy) and Budapest (Hungary) have occasional blooms of Pseudomonas-dominated communities, accounting for up to ~95% of sample DNA. Seasonal shifts and blooms present challenges for effective sewage surveillance. We find that bacteria of known shared origin, like human gut microbiota, form communities, suggesting the potential for source-attributing novel species and their ARGs through network community analysis. This could significantly improve AMR tracking in urban environments.
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Affiliation(s)
- Ágnes Becsei
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Alessandro Fuschi
- Department of Physics and Astronomy (DIFA), University of Bologna, Bologna, Italy
| | - Saria Otani
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Ravi Kant
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdynia, Poland
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ilja Weinstein
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Patricia Alba
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Rome, Italy
| | - József Stéger
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dávid Visontai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Christian Brinch
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Miranda de Graaf
- Viroscience Department and Pandemic and Disaster Preparedness Research Centre, Erasmus MC, Rotterdam, The Netherlands
| | - Claudia M E Schapendonk
- Viroscience Department and Pandemic and Disaster Preparedness Research Centre, Erasmus MC, Rotterdam, The Netherlands
| | - Antonio Battisti
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Rome, Italy
| | - Alessandra De Cesare
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (BO), Italy
| | - Chiara Oliveri
- Department of Physics and Astronomy (DIFA), University of Bologna, Bologna, Italy
| | - Fulvia Troja
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (BO), Italy
| | - Tarja Sironen
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Frédérique Pasquali
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Krisztián Bányai
- Pathogen Discovery Group, HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary
| | | | - Péter Pollner
- Data-Driven Health Division of National Laboratory for Health Security, Health Services Management Training Centre, Semmelweis University, Budapest, Hungary
- Department of Biological Physics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Alessandra Merlotti
- Department of Physics and Astronomy (DIFA), University of Bologna, Bologna, Italy
| | - Marion Koopmans
- Viroscience Department and Pandemic and Disaster Preparedness Research Centre, Erasmus MC, Rotterdam, The Netherlands
| | - Istvan Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Daniel Remondini
- Department of Physics and Astronomy (DIFA), University of Bologna, Bologna, Italy
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Lyngby, Denmark.
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Olson MA, Cullimore C, Hutchison WD, Grimsrud A, Nobrega D, De Buck J, Barkema HW, Wilson E, Pickett BE, Erickson DL. Genes associated with fitness and disease severity in the pan-genome of mastitis-associated Escherichia coli. Front Microbiol 2024; 15:1452007. [PMID: 39268542 PMCID: PMC11390585 DOI: 10.3389/fmicb.2024.1452007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/19/2024] [Indexed: 09/15/2024] Open
Abstract
Introduction Bovine mastitis caused by Escherichia coli compromises animal health and inflicts substantial product losses in dairy farming. It may manifest as subclinical through severe acute disease and can be transient or persistent in nature. Little is known about bacterial factors that impact clinical outcomes or allow some strains to outcompete others in the mammary gland (MG) environment. Mastitis-associated E. coli (MAEC) may have distinctive characteristics which may contribute to the varied nature of the disease. Given their high levels of intraspecies genetic variability, virulence factors of commonly used MAEC model strains may not be relevant to all members of this group. Methods In this study, we sequenced the genomes of 96 MAEC strains isolated from cattle with clinical mastitis (CM). We utilized clinical severity data to perform genome-wide association studies to identify accessory genes associated with strains isolated from mild or severe CM, or with high or low competitive fitness during in vivo competition assays. Genes associated with mastitis pathogens or commensal strains isolated from bovine sources were also identified. Results A type-2 secretion system (T2SS) and a chitinase (ChiA) exported by this system were strongly associated with pathogenic isolates compared with commensal strains. Deletion of chiA from MAEC isolates decreased their adherence to cultured bovine mammary epithelial cells. Discussion The increased fitness associated with strains possessing this gene may be due to better attachment in the MG. Overall, these results provide a much richer understanding of MAEC and suggest bacterial processes that may underlie the clinical diversity associated with mastitis and their adaptation to this unique environment.
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Affiliation(s)
- Michael A Olson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Caz Cullimore
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Weston D Hutchison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Aleksander Grimsrud
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Diego Nobrega
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jeroen De Buck
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Herman W Barkema
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Eric Wilson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Brett E Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - David L Erickson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
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49
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Hiraoka Furuya Y, Abo H, Matsuda M, Harada S, Kumakawa M, Shirakawa T, Ozawa M, Kawanishi M, Sekiguchi H, Shimazaki Y. Genomic characterization of third-generation cephalosporin-resistant Escherichia coli strains isolated from diseased dogs and cats: Report from Japanese Veterinary Antimicrobial Resistance Monitoring. Vet Microbiol 2024; 298:110220. [PMID: 39208596 DOI: 10.1016/j.vetmic.2024.110220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 07/22/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
This study investigates the genomic characteristics of canine and feline cefotaxime (CTX, a third-generation cephalosporin)-resistant Escherichia coli using the JVARM, Japanese Veterinary Antimicrobial Resistance Monitoring System, a nationwide monitoring. In this study, whole-genome sequencing (WGS) was performed on 51 canine and 45 feline CTX-resistant E. coli isolates, with certain isolates subjected to pulsed-field gel electrophoresis with S1 nuclease for plasmid-chromosome separation. The most common blaCTX-M genes were blaCTX-M-27 (dogs: 11/51 [21.6 %]; cat: 10/45 [22.2 %]), followed by blaCTX-M-14 (dogs: 10/51 [19.6 %]; cats: 10/45 [22.2 %]), and blaCTX-M-15 (dogs: 9/51 [17.6 %]; cats: 5/45 [11.1 %]). Besides β-lactamase genes, all isolates harbored mdf(A), a multidrug efflux pump, with resistance genes for aminoglycosides, sulfonamides, trimethoprims, macrolides and tetracyclines. None of the isolates had carbapenemase genes, such as blaOXA-48, blaNDM, and blaIMP, whereas most of the isolates showed double mutations in gyrA and parC, which affected quinolone resistance. For the isolates separately analyzed for plasmid and chromosomal DNA via WGS, the majority of CTX-M genes were present on the plasmids. Some plasmids also harbored the same combination of resistance genes and plasmid replicon type, although they differed from isolates derived from different areas of Japan. The predominant plasmids were blaCTX-M-27,aadA5, aph(6)-Id, aph(3")-Ib, sul1, sul2, tet(A), dfrA17, and mph(A) on IncF. The predominant combination of ST131, O25:H4, and B2 isolates comprised the largest cluster in the minimum spanning tree and the ST131 E. coli harboring blaCTX-M-27 from human in Japan was closely related to these isolates. The results indicated that CTX-resistant canine and feline E. coli harbored multiple plasmids carrying the same combination of resistance genes and emphasizes the need to prevent the spread. DATA AVAILABILITY: All raw short-read sequence data have been deposited in the DNA Data Bank of Japan. (DRR Run No, DRR335726-335821).
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Affiliation(s)
- Yukari Hiraoka Furuya
- National Veterinary Assay Laboratory, Ministry of Agriculture Forestry and Fisheries, 1-15-1 Tokura, Kokubunji, Tokyo 185-8511, Japan.
| | - Hitoshi Abo
- National Veterinary Assay Laboratory, Ministry of Agriculture Forestry and Fisheries, 1-15-1 Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Mari Matsuda
- National Veterinary Assay Laboratory, Ministry of Agriculture Forestry and Fisheries, 1-15-1 Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Saki Harada
- National Veterinary Assay Laboratory, Ministry of Agriculture Forestry and Fisheries, 1-15-1 Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Mio Kumakawa
- National Veterinary Assay Laboratory, Ministry of Agriculture Forestry and Fisheries, 1-15-1 Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Takahiro Shirakawa
- National Veterinary Assay Laboratory, Ministry of Agriculture Forestry and Fisheries, 1-15-1 Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Manao Ozawa
- National Veterinary Assay Laboratory, Ministry of Agriculture Forestry and Fisheries, 1-15-1 Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Michiko Kawanishi
- National Veterinary Assay Laboratory, Ministry of Agriculture Forestry and Fisheries, 1-15-1 Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Hideto Sekiguchi
- National Veterinary Assay Laboratory, Ministry of Agriculture Forestry and Fisheries, 1-15-1 Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Yoko Shimazaki
- National Veterinary Assay Laboratory, Ministry of Agriculture Forestry and Fisheries, 1-15-1 Tokura, Kokubunji, Tokyo 185-8511, Japan
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50
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Hong Tuan Ha AS, Mammeri A, Plainvert C, Charfi R, Poyart C, Tazi A, Mammeri H. Clinical emergence of a novel extended-spectrum variant deriving from the OXY-1 β-lactamase. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04922-8. [PMID: 39172287 DOI: 10.1007/s10096-024-04922-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/06/2024] [Indexed: 08/23/2024]
Abstract
The genomic comparison of two Klebsiella michiganensis clinical isolates recovered from the same patient, one resistant to piperacillin-tazobactam and intermediate to cefotaxime, the other resistant to ceftazidime but susceptible to piperacillin-tazobactam, revealed one mutation in the blaOXY-1-24 gene accounting for a L169M substitution in the Ω loop. Cloning experiment in Escherichia coli demonstrated the contribution of this mutation to the hydrolysis spectrum extension towards ceftazidime and cefepime, whereas the resistance to piperacillin-tazobactam was reduced. To the best of our knowledge, this study shows for the first time that ceftazidime resistance can occur in vivo from OXY-1 precursor by structural alteration.
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Affiliation(s)
- Anne-Sophie Hong Tuan Ha
- Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Site Cochin, 27 rue du Faubourg Saint-Jacques, Paris, 75014, France
| | - Alice Mammeri
- INSERM, CNRS, Institut Necker Enfants Malades, Université Paris Cité, , Paris, 75015, France
| | - Céline Plainvert
- Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Site Cochin, 27 rue du Faubourg Saint-Jacques, Paris, 75014, France
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris Cité, Paris, France
| | - Rym Charfi
- Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Site Cochin, 27 rue du Faubourg Saint-Jacques, Paris, 75014, France
| | - Claire Poyart
- Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Site Cochin, 27 rue du Faubourg Saint-Jacques, Paris, 75014, France
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris Cité, Paris, France
| | - Asmaa Tazi
- Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Site Cochin, 27 rue du Faubourg Saint-Jacques, Paris, 75014, France
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris Cité, Paris, France
| | - Hedi Mammeri
- Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Site Cochin, 27 rue du Faubourg Saint-Jacques, Paris, 75014, France.
- INSERM, CNRS, Institut Necker Enfants Malades, Université Paris Cité, , Paris, 75015, France.
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