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Furlan JPR, da Silva Rosa R, Ramos MS, Dos Santos LDR, Savazzi EA, Stehling EG. Emergence of carbapenem-resistant Klebsiella pneumoniae species complex from agrifood systems: detection of ST6326 co-producing KPC-2 and NDM-1. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:7347-7354. [PMID: 38651793 DOI: 10.1002/jsfa.13555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND Klebsiella pneumoniae species complex (KpSC) is an important disseminator of carbapenemase-encoding genes, mainly blaKPC-2 and blaNDM-1, from hospitals to the environment. Consequently, carbapenem-resistant strains can be spread through the agrifood system, raising concerns about food safety. This study therefore aimed to isolate carbapenem-resistant KpSC strains from the agricultural and environmental sectors and characterize them using phenotypic, molecular, and genomic analyses. RESULTS Klebsiella pneumoniae and Klebsiella quasipneumoniae strains isolated from soils used for lemon, guava, and fig cultivation, and from surface waters, displayed an extensive drug-resistance profile and carried blaKPC-2, blaNDM-1, or both. In addition to carbapenemase-encoding genes, KpSC strains harbor a broad resistome (antimicrobial resistance and metal tolerance) and present putative hypervirulence. Soil-derived K. pneumoniae strains were assigned as high-risk clones (ST11 and ST307) and harbored the blaKPC-2 gene associated with Tn4401b and Tn3-like elements on IncN-pST15 and IncX5 plasmids. In surface waters, the coexistence of blaKPC-2 and blaNDM-1 genes was identified in K. pneumoniae ST6326, a new carbapenem-resistant regional Brazilian clone. In this case, blaKPC-2 with Tn4401a isoform and blaNDM-1 associated with a Tn125-like transposon were located on different plasmids. Klebsiella quasipneumoniae ST526 also presented the blaNDM-1 gene associated with a Tn3000 transposon on an IncX3 plasmid. CONCLUSION These findings provide a warning regarding the transmission of carbapenemase-positive KpSC across the agricultural and environmental sectors, raising critical food safety and environmental issues. © 2024 Society of Chemical Industry.
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Rafael da Silva Rosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Lucas David Rodrigues Dos Santos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | | | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
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2
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Sabtcheva S, Stoikov I, Ivanov IN, Donchev D, Lesseva M, Georgieva S, Teneva D, Dobreva E, Christova I. Genomic Characterization of Carbapenemase-Producing Enterobacter hormaechei, Serratia marcescens, Citrobacter freundii, Providencia stuartii, and Morganella morganii Clinical Isolates from Bulgaria. Antibiotics (Basel) 2024; 13:455. [PMID: 38786183 PMCID: PMC11117914 DOI: 10.3390/antibiotics13050455] [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: 04/25/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Carbapenemase-producing Enterobacter spp. Serratia marcescens, Citrobacter freundii, Providencia spp., and Morganella morganii (CP-ESCPM) are increasingly identified as causative agents of nosocomial infections but are still not under systematic genomic surveillance. In this study, using a combination of whole-genome sequencing and conjugation experiments, we sought to elucidate the genomic characteristics and transferability of resistance genes in clinical CP-ESCPM isolates from Bulgaria. Among the 36 sequenced isolates, NDM-1 (12/36), VIM-4 (11/36), VIM-86 (8/36), and OXA-48 (7/36) carbapenemases were identified; two isolates carried both NDM-1 and VIM-86. The majority of carbapenemase genes were found on self-conjugative plasmids. IncL plasmids were responsible for the spread of OXA-48 among E. hormaechei, C. freundii, and S. marcescens. IncM2 plasmids were generally associated with the spread of NDM-1 in C. freundii and S. marcescens, and also of VIM-4 in C. freundii. IncC plasmids were involved in the spread of the recently described VIM-86 in P. stuartii isolates. IncC plasmids carrying blaNDM-1 and blaVIM-86 were observed too. blaNDM-1 was also detected on IncX3 in S. marcescens and on IncT plasmid in M. morganii. The significant resistance transfer rates we observed highlight the role of the ESCPM group as a reservoir of resistance determinants and stress the need for strengthening infection control measures.
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Affiliation(s)
- Stefana Sabtcheva
- Laboratory for Clinical Microbiology, National Oncology Center, 1797 Sofia, Bulgaria; (I.S.); (S.G.)
| | - Ivan Stoikov
- Laboratory for Clinical Microbiology, National Oncology Center, 1797 Sofia, Bulgaria; (I.S.); (S.G.)
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Ivan N. Ivanov
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Deyan Donchev
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Magdalena Lesseva
- Department of Microbiology, University Multiprofile Hospital for Active Treatment and Emergency Medicine “N. I. Pirogov”, 1606 Sofia, Bulgaria;
| | - Sylvia Georgieva
- Laboratory for Clinical Microbiology, National Oncology Center, 1797 Sofia, Bulgaria; (I.S.); (S.G.)
| | - Deana Teneva
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Elina Dobreva
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Iva Christova
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
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3
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Zhu J, Wang G, Li M. Outbreak of NDM-5-producing Klebsiella pneumoniae ST307: an emerging high-risk antimicrobial resistance clone in Shanghai, China. mSystems 2024; 9:e0136923. [PMID: 38506533 PMCID: PMC11019902 DOI: 10.1128/msystems.01369-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/08/2024] [Indexed: 03/21/2024] Open
Abstract
The high-risk clone Klebsiella pneumoniae ST307, associated with various carbapenem resistance genes, exhibits a global distribution and prevalence. However, in China, it has remained sporadic and has rarely been detected. In this study, we reported an outbreak caused by nine ST307 CRKP isolates harboring blaNDM-5 in Shanghai, China, in 2022. We employed antimicrobial susceptibility testing, conjugation assay, whole-genome sequencing (WGS) and comparative genomics, phylogenetic analysis, and fitness and virulence comparison to further characterize the isolates causing the outbreak. Besides blaNDM-5, these nine isolates co-carried blaCTX-M-15 and blaDHA-1, exhibiting nearly identical resistance profiles with high-level resistance to carbapenems and ceftazidime/avibactam, while showing susceptibility to colistin and tigecycline. blaNDM-5 was located on an IncX3 plasmid of 45,403 bp with a high frequency of conjugative ability. Phylogenetic and single-nucleotide polymorphism (SNP) analysis indicated the nature of clonal transmission with a maximum of five SNPs between these nine isolates, and they were closely related to strains obtained from the United States. ST307 isolates in our study showed a relatively lower virulence but higher growth rates and certain adaptability compared with ST11 isolates. Clinical investigation revealed that shared nursing staff in a mixed emergency intensive care unit ward and doctors' movement between wards might be responsible for the outbreak. The nonexistence before and sudden emergence of ST307 suggested that the currently circulating ST307 clone was a newly introduced superbug in our hospital. In conclusion, we revealed that blaNDM-5-producing ST307 CRKP isolates, a globally significant high-risk clone, are spreading in China, posing a substantial threat to public health.IMPORTANCEThe high-risk clone ST307, associated with various carbapenemases, including KPC, NDM, and OXA, has a global distribution. However, it is rarely reported in China, let alone causing outbreaks. Here, we found an outbreak caused by the clonal transmission of nine ST307 CRKP isolates. Clinical investigation revealed that shared nurses in a mixed emergency intensive care unit ward and doctors' movement between wards might be responsible for the outbreak. In our study, the nine NDM-5-producing ST307 isolates exhibited high-level resistance to carbapenems and ceftazidime-avibactam, high conjugative ability to Escherichia coli J53, and certain adaptability to environment, phylogenetically closet to the United States. All these features make ST307 clone the next successful clone comparable to ST11 clone in China. Therefore, it is imperative for us to vigilantly monitor the prevalence of carbapenem-resistant Klebsiella pneumoniae and promptly implement measures to control the spread of K. pneumoniae ST307 in China.
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Affiliation(s)
- Junying Zhu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guangyu Wang
- Department of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Quinones-Olvera N, Owen SV, McCully LM, Marin MG, Rand EA, Fan AC, Martins Dosumu OJ, Paul K, Sanchez Castaño CE, Petherbridge R, Paull JS, Baym M. Diverse and abundant phages exploit conjugative plasmids. Nat Commun 2024; 15:3197. [PMID: 38609370 PMCID: PMC11015023 DOI: 10.1038/s41467-024-47416-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 65 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the evolutionarily promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.
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Affiliation(s)
- Natalia Quinones-Olvera
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Siân V Owen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Lucy M McCully
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Maximillian G Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eleanor A Rand
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Alice C Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Boston University, Boston, MA, 02215, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Oluremi J Martins Dosumu
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Kay Paul
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Cleotilde E Sanchez Castaño
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Rachel Petherbridge
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jillian S Paull
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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5
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Leelapsawas C, Sroithongkham P, Payungporn S, Nimsamer P, Yindee J, Collaud A, Perreten V, Chanchaithong P. First report of blaOXA-181-carrying IncX3 plasmids in multidrug-resistant Enterobacter hormaechei and Serratia nevei recovered from canine and feline opportunistic infections. Microbiol Spectr 2024; 12:e0358923. [PMID: 38319115 PMCID: PMC10913469 DOI: 10.1128/spectrum.03589-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/14/2024] [Indexed: 02/07/2024] Open
Abstract
Whole-genome sequence analysis of six Enterobacter hormaechei and two Serratia nevei strains, using a hybrid assembly of Illumina and Oxford Nanopore Technologies sequencing, revealed the presence of the epidemic blaOXA-181-carrying IncX3 plasmids co-harboring qnrS1 and ∆ere(A) genes, as well as multiple multidrug resistance (MDR) plasmids disseminating in all strains, originated from dogs and cats in Thailand. The subspecies and sequence types (ST) of the E. hormaechei strains recovered from canine and feline opportunistic infections included E. hormaechei subsp. xiangfangensis ST171 (n = 3), ST121 (n = 1), and ST182 (n = 1), as well as E. hormaechei subsp. steigerwaltii ST65 (n = 1). Five of the six E. hormaechei strains harbored an identical 51,479-bp blaOXA-181-carrying IncX3 plasmid. However, the blaOXA-181 plasmid (pCUVET22-969.1) of the E. hormaechei strain CUVET22-969 presented a variation due to the insertion of ISKpn74 and ISSbo1 into the virB region. Additionally, the blaOXA-181 plasmids of S. nevei strains were nearly identical to the others at the nucleotide level, with ISEcl1 inserted upstream of the qnrS1 gene. The E. hormaechei and S. nevei lineages from canine and feline origins might acquire the epidemic blaOXA-181-carrying IncX3 and MDR plasmids, which are shared among Enterobacterales, contributing to the development of resistance. These findings suggest the spillover of significant OXA-181-encoding plasmids to these bacteria, causing severe opportunistic infections in dogs and cats in Thailand. Surveillance and effective hygienic practice, especially in hospitalized animals and veterinary hospitals, should be urgently implemented to prevent the spread of these plasmids in healthcare settings and communities. IMPORTANCE blaOXA-181 is a significant carbapenemase-encoding gene, usually associated with an epidemic IncX3 plasmid found in Enterobacterales worldwide. In this article, we revealed six carbapenemase-producing (CP) Enterobacter hormaechei and two CP Serratia nevei strains harboring blaOXA-181-carrying IncX3 and multidrug resistance plasmids recovered from dogs and cats in Thailand. The carriage of these plasmids can promote extensively drug-resistant properties, limiting antimicrobial treatment options in veterinary medicine. Since E. hormaechei and S. nevei harboring blaOXA-181-carrying IncX3 plasmids have not been previously reported in dogs and cats, our findings provide the first evidence of dissemination of the epidemic plasmids in these bacterial species isolated from animal origins. Pets in communities can serve as reservoirs of significant antimicrobial resistance determinants. This situation places a burden on antimicrobial treatment in small animal practice and poses a public health threat.
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Affiliation(s)
- Chavin Leelapsawas
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Parinya Sroithongkham
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Sunchai Payungporn
- Center of Excellence in Systems Microbiology (CESM), Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pattaraporn Nimsamer
- Center of Excellence in Systems Microbiology (CESM), Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jitrapa Yindee
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Alexandra Collaud
- Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Pattrarat Chanchaithong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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AL-Busaidi B, AL-Muzahmi M, AL-Shabibi Z, Rizvi M, AL-Rashdi A, AL-Jardani A, Farzand R, AL-Jabri Z. Hypervirulent Capsular Serotypes K1 and K2 Klebsiella pneumoniae Strains Demonstrate Resistance to Serum Bactericidal Activity and Galleria mellonella Lethality. Int J Mol Sci 2024; 25:1944. [PMID: 38339222 PMCID: PMC10855873 DOI: 10.3390/ijms25031944] [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: 01/05/2024] [Revised: 01/28/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) is a variant that has been increasingly linked to severe, life-threatening infections including pyogenic liver abscess and bloodstream infections. HvKps belonging to the capsular serotypes K1 and K2 have been reported worldwide, however, very scarce studies are available on their genomics and virulence. In the current study, we report four hypermucoviscous extended-spectrum β-lactamase-producing hvKp clinical strains of capsular serotype K1 and K2 isolated from pus and urine of critically ill patients in tertiary care hospitals in Oman. These strains belong to diverse sequence types (STs), namely ST-23(K1), ST-231(K2), ST-881(K2), and ST-14(K2). To study their virulence, a Galleria mellonella model and resistance to human serum killing were used. The G. mellonella model revealed that the K1/ST-23 isolate was the most virulent, as 50% of the larvae died in the first day, followed by isolate K2/ST-231 and K2/ST-14, for which 75% and 50% of the larvae died in the second day, respectively. Resistance to human serum killing showed there was complete inhibition of bacterial growth of all four isolates by the end of the first hour and up to the third hour. Whole genome sequencing (WGS) revealed that hvKp strains display a unique genetic arrangement of k-loci. Whole-genome single-nucleotide polymorphism-based phylogenetic analysis revealed that these hvKp isolates were phylogenetically distinct, belonging to diverse clades, and belonged to different STs in comparison to global isolates. For ST-23(K1), ST-231(K2), ST-881(K2), and ST-14(K2), there was a gradual decrease in the number of colonies up to the second to third hour, which indicates neutralization of bacterial cells by the serum components. However, this was followed by a sudden increase of bacterial growth, indicating possible resistance of bacteria against human serum bactericidal activity. This is the first report from Oman detailing the WGS of hvKp clinical isolates and assessing their resistance and virulence genomics, which reinforce our understanding of their epidemiology and dissemination in clinical settings.
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Affiliation(s)
- Basaier AL-Busaidi
- Microbiology and Immunology Diagnostic Laboratory, Department of Microbiology and Immunology, Sultan Qaboos University Hospital, Muscat 123, Oman;
| | | | - Zahra AL-Shabibi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University Hospital, Muscat 123, Oman;
| | - Meher Rizvi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, Oman
| | - Azza AL-Rashdi
- Central Public Health Laboratory, Department of Medical Microbiology, Ministry of Health, Muscat 100, Oman; (A.A.-R.); (A.A.-J.)
| | - Amina AL-Jardani
- Central Public Health Laboratory, Department of Medical Microbiology, Ministry of Health, Muscat 100, Oman; (A.A.-R.); (A.A.-J.)
| | - Robeena Farzand
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK;
| | - Zaaima AL-Jabri
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University Hospital, Muscat 123, Oman;
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The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2021-2022. EFSA J 2024; 22:e8583. [PMID: 38419967 PMCID: PMC10900121 DOI: 10.2903/j.efsa.2024.8583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
This report by the European Food Safety Authority and the European Centre for Disease prevention and Control, provides an overview of the main findings of the 2021-2022 harmonised Antimicrobial Resistance (AMR) monitoring in Salmonella spp., Campylobacter jejuni and C. coli from humans and food-producing animals (broilers, laying hens and fattening turkeys, fattening pigs and cattle under one year of age) and relevant meat thereof. For animals and meat thereof, AMR data on indicator commensal Escherichia coli, presumptive extended-spectrum beta-lactamases (ESBL)-/AmpC beta-lactamases (AmpC)-/carbapenemase (CP)-producing E. coli, and the occurrence of methicillin-resistant Staphylococcus aureus (MRSA) are also analysed. Generally, resistance levels differed greatly between reporting countries and antimicrobials. Resistance to commonly used antimicrobials was frequently found in Salmonella and Campylobacter isolates from humans and animals. In humans, increasing trends in resistance to one of two critically antimicrobials (CIA) for treatment was observed in poultry-associated Salmonella serovars and Campylobacter, in at least half of the reporting countries. Combined resistance to CIA was however observed at low levels except in some Salmonella serovars and in C. coli from humans and animals in some countries. While CP-producing Salmonella isolates were not detected in animals in 2021-2022, nor in 2021 for human cases, in 2022 five human cases of CP-producing Salmonella were reported (four harbouring bla OXA-48 or bla OXA-48-like genes). The reporting of a number of CP-producing E. coli isolates (harbouring bla OXA-48, bla OXA-181, bla NDM-5 and bla VIM-1 genes) in fattening pigs, cattle under 1 year of age, poultry and meat thereof by a limited number of MSs (5) in 2021 and 2022, requires a thorough follow-up. The temporal trend analyses in both key outcome indicators (rate of complete susceptibility and prevalence of ESBL-/AmpC-producers in E. coli) showed an encouraging progress in reducing AMR in food-producing animals in several EU MSs over the last 7 years.
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Bartsch LJ, Borowiak M, Deneke C, Gruetzke J, Hammerl JA, Malorny B, Szabo I, Alter T, Nguyen KK, Fischer J. Genetic characterization of a multidrug-resistant Salmonella enterica serovar Agona isolated from a dietary supplement in Germany. Front Microbiol 2023; 14:1284929. [PMID: 38033583 PMCID: PMC10686068 DOI: 10.3389/fmicb.2023.1284929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023] Open
Abstract
Salmonella enterica subsp. enterica serovar Agona has a history of causing food-borne outbreaks and any emergence of multidrug-resistant (MDR) isolates in novel food products is of concern. Particularly, in food products frequently consumed without sufficient heating prior to consumption. Here, we report about the MDR isolate, 18-SA00377, which had been isolated from a dietary supplement in Germany in 2018 and submitted to the German National Reference Laboratory for Salmonella. WGS-based comparative genetic analyses were conducted to find a potential reservoir of the isolate itself or mobile genetic elements associated with MDR. As a phylogenetic analysis did not yield any closely related S. Agona isolates, either globally or from Germany, a detailed analysis of the largest plasmid (295,499 bp) was performed as it is the main carrier of resistances. A combined approach of long-read and short-read sequencing enabled the assembly of the isolate's chromosome and its four plasmids. Their characterization revealed the presence of 23 different antibiotic resistance genes (ARGs), conferring resistance to 12 different antibiotic drug classes, as well as genes conferring resistance to six different heavy metals. The largest plasmid, pSE18-SA00377-1, belongs to the IncHI2 plasmid family and carries 16 ARGs, that are organized as two distinct clusters, with each ARG associated with putative composite transposons. Through a two-pronged approach, highly similar plasmids to pSE18-SA00377-1 were identified in the NCBI database and a search for Salmonella isolates with a highly similar ARG resistance profile was conducted. Mapping and structural comparisons between pSE18-SA00377-1 and these plasmids and Salmonella isolates showed that both the plasmid backbone and identical or similar ARG clusters can be found not only in Salmonella isolates, originating mostly from a wide variety of livestock, but also in a diverse range of bacterial genera of varying geographical origins and isolation sources. Thus, it can be speculated that the host range of pSE18-SA00377-1 is not restricted to Salmonella and its spread already occurred in different bacterial populations. Overall, this hints at a complex history for pSE18-SA00377-1 and highlights the importance of surveilling multidrug-resistant S. enterica isolates, especially in novel food items that are not yet heavily regulated.
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Affiliation(s)
- Lee Julia Bartsch
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Maria Borowiak
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Carlus Deneke
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Josephine Gruetzke
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jens-Andre Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Burkhard Malorny
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Istvan Szabo
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Thomas Alter
- Institute of Food Safety and Food Hygiene, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | - Jennie Fischer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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9
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Furlan JPR, Stehling EG. Genomic Insights into Pluralibacter gergoviae Sheds Light on Emergence of a Multidrug-Resistant Species Circulating between Clinical and Environmental Settings. Pathogens 2023; 12:1335. [PMID: 38003800 PMCID: PMC10675545 DOI: 10.3390/pathogens12111335] [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: 09/15/2023] [Revised: 10/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Pluralibacter gergoviae is a member of the Enterobacteriaceae family that has been reported sporadically. Although P. gergoviae strains exhibiting multidrug-resistant profiles have been identified an in-depth genomic analysis focusing on antimicrobial resistance (AMR) has been lacking, and was therefore performed in this study. Forty-eight P. gergoviae strains, isolated from humans, animals, foods, and the environment during 1970-2023, were analyzed. A large number of single-nucleotide polymorphisms were found, indicating a highly diverse population. Whilst P. gergoviae strains were found to be circulating at the One Health interface, only human and environmental strains exhibited multidrug resistance genotypes. Sixty-one different antimicrobial resistance genes (ARGs) were identified, highlighting genes encoding mobile colistin resistance, carbapenemases, and extended-spectrum β-lactamases. Worryingly, the co-occurrence of mcr-9.1, blaKPC-2, blaCTX-M-9, and blaSHV-12, as well as mcr-10.1, blaNDM-5, and blaSHV-7, was detected. Plasmid sequences were identified as carrying clinically important ARGs, evidencing IncX3 plasmids harboring blaKPC-2, blaNDM-5, or blaSHV-12 genes. Virulence genotyping underlined P. gergoviae as being a low-virulence species. In this regard, P. gergoviae is emerging as a new multidrug-resistant species belonging to the Enterobacteriaceae family. Therefore, continuous epidemiological genomic surveillance of P. gergoviae is required.
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Affiliation(s)
| | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil;
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10
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Furlan JPR, da Silva Rosa R, Ramos MS, Dos Santos LDR, Savazzi EA, Stehling EG. Genomic features of an extensively drug-resistant and NDM-1-positive Klebsiella pneumoniae ST340 isolated from river water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:114678-114684. [PMID: 37845596 DOI: 10.1007/s11356-023-30374-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023]
Abstract
The environmental contamination plays a significant role in the emergence of antimicrobial resistance. In this study, we report a genomic analysis of an extensively drug-resistant and blaNDM-1-producing Klebsiella pneumoniae (EW807) strain recovered from a surface water sample. Strain EW807 belonged to sequence type (ST) 340 and serotype O4:KL15, a high-risk clone of the clonal group 258. This strain carried a broad resistome, including blaNDM-1 and blaCTX-M-15. The core genome multilocus sequence typing phylogenetic analysis revealed that the EW807 strain was most related to strains from Brazil and the USA. An IncX3 plasmid was identified harboring the blaNDM-1 gene, while an IncFIB(K) plasmid was detected carrying the blaCTX-M-15 in addition to multidrug resistance and multimetal tolerance regions. IncX3 and IncFIB(K) plasmids shared high similarity with plasmids from a human in China and a dog in Brazil, respectively. The regions harboring the blaNDM-1 and blaCTX-M-15 genes contained sequences from the Tn3 family. These findings suggest that IncX3 plasmid could play a role in the spread of NDM-1 in a post-pandemic scenario. To the best of our knowledge, this is the first report of blaNDM-1-producing K. pneumoniae ST340 O4:KL15 strain in the environment. Therefore, the presence of high-risk clones of K. pneumoniae carrying carbapenemases in the environment requires strict surveillance.
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Rafael da Silva Rosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Lucas David Rodrigues Dos Santos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | | | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil.
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11
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Yang Y, Liu H, Chen L, Mao M, Zhang X, Zhou L, Duan D, Li X, Zhou H. Molecular characterization and comparison of bla NDM-1-carrying and bla NDM-5-harboring IncX3-type plasmids in carbapenem-resistant Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0102823. [PMID: 37623430 PMCID: PMC10581223 DOI: 10.1128/spectrum.01028-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/14/2023] [Indexed: 08/26/2023] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP), which harbors the bla NDM plasmid, has been reported extensively and is considered a global threat clinically. However, characterization and comparisons of bla NDM-1-carrying and bla NDM-5-harboring IncX3-type plasmids in CRKP are lacking. Here, we systematically compared the differences in the characteristics, genetic backgrounds, transferability, and fitness costs between bla NDM-1-carrying and bla NDM-5-carrying plasmids in K. pneumoniae isolates. Fifteen NDM-producing CRKP isolates were recovered from 1376 CRKP isolates between 2019 and 2021, of which 4 were positive for bla NDM-1 and 11 were positive for bla NDM-5. All strains were highly resistant to carbapenem but remained susceptible to tigecycline and colistin. Core-genome-based phylogenetic analyses revealed that these strains were not clonally related. Whole-genome sequencing showed that bla NDM-1 and bla NDM-5 were located on ~54 kb and ~46 kb IncX3-type plasmids, respectively. The backbone, genetic context, and fitness cost of the bla NDM-1-bearing plasmid were highly similar to those of the bla NDM-5-carrying plasmid, but the transferability of the bla NDM-1-positive plasmid was greater than that of the bla NDM-5-positive plasmid. In conclusion, the transmission of bla NDM-1 or bla NDM-5 is mainly disseminated by plasmids rather than clonal spread. The high transfer frequency of the IncX3 plasmid facilitates the prevalence and dissemination of NDM-KP among Enterobacteriaceae. IMPORTANCE The emergence of NDM-producing Klebsiella pneumoniae is a severe challenge to public health. The widespread presence of bla NDM-1 and bla NDM-5 in Enterobacteriaceae has aroused broad concern. In this study, we performed molecular characterization of bla NDM-1-carrying and bla NDM-5-harboring IncX3-type plasmids in carbapenem-resistant Klebsiella pneumoniae (CRKP) and compared their phenotypes between strains with different bla NDM subtype. Our findings highlight the importance of IncX3-type plasmids in the transfer of the bla NDM-1 and bla NDM-5 genes and demonstrate that the bla NDM-1 plasmid possesses higher transfer ability. These data will provide important insights into carbapenem resistance gene transfer via plasmids and their further spread in clinical settings.
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Affiliation(s)
- Yunxing Yang
- Department of Clinical Laboratory, Affiliated Hangzhou First People’s Hospital, Zhejiang School of Medicine, Hangzhou, China
| | - Haiyang Liu
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - Lingxia Chen
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - Minjie Mao
- Department of Clinical Laboratory, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Xiaofan Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - Longjie Zhou
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - Darong Duan
- Department of Laboratory Medicine, Huangyan Hospital of Wenzhou Medical University, Taizhou First People’ s Hospital, Taizhou, Zhejiang, China
| | - Xi Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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12
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Shelenkov A, Mikhaylova Y, Voskanyan S, Egorova A, Akimkin V. Whole-Genome Sequencing Revealed the Fusion Plasmids Capable of Transmission and Acquisition of Both Antimicrobial Resistance and Hypervirulence Determinants in Multidrug-Resistant Klebsiella pneumoniae Isolates. Microorganisms 2023; 11:1314. [PMID: 37317293 DOI: 10.3390/microorganisms11051314] [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: 03/23/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Klebsiella pneumoniae, a member of the Enterobacteriaceae family, has become a dangerous pathogen accountable for a large fraction of the various infectious diseases in both clinical and community settings. In general, the K. pneumoniae population has been divided into the so-called classical (cKp) and hypervirulent (hvKp) lineages. The former, usually developing in hospitals, can rapidly acquire resistance to a wide spectrum of antimicrobial drugs, while the latter is associated with more aggressive but less resistant infections, mostly in healthy humans. However, a growing number of reports in the last decade have confirmed the convergence of these two distinct lineages into superpathogen clones possessing the properties of both, and thus imposing a significant threat to public health worldwide. This process is associated with horizontal gene transfer, in which plasmid conjugation plays a very important role. Therefore, the investigation of plasmid structures and the ways plasmids spread within and between bacterial species will provide benefits in developing prevention measures against these powerful pathogens. In this work, we investigated clinical multidrug-resistant K. pneumoniae isolates using long- and short-read whole-genome sequencing, which allowed us to reveal fusion IncHI1B/IncFIB plasmids in ST512 isolates capable of simultaneously carrying hypervirulence (iucABCD, iutA, prmpA, peg-344) and resistance determinants (armA, blaNDM-1 and others), and to obtain insights into their formation and transmission mechanisms. Comprehensive phenotypic, genotypic and phylogenetic analysis of the isolates, as well as of their plasmid repertoire, was performed. The data obtained will facilitate epidemiological surveillance of high-risk K. pneumoniae clones and the development of prevention strategies against them.
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Affiliation(s)
- Andrey Shelenkov
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Yulia Mikhaylova
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Shushanik Voskanyan
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Anna Egorova
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Vasiliy Akimkin
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
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13
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Xiang Y, Liu Z, Yu G, Song Y, Li Y, Geng X, Ma L, Guo J, Tan L, Chen P. Genetic characteristic of coexisting of mcr-1 and blaNDM-5 in Escherichia coli isolates from lesion-bearing animal organs. Front Microbiol 2023; 14:1116413. [PMID: 37007493 PMCID: PMC10050402 DOI: 10.3389/fmicb.2023.1116413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/21/2023] [Indexed: 03/17/2023] Open
Abstract
The coexistence of mcr-1 and blaNDM-5 in the plasmid of Escherichia coli has been widely reported and such strains have been mainly isolated from animal and human feces. However, few reports have focused on the genetic diversity of mcr-1-carrying chromosomes and blaNDM-5-carrying plasmids in E. coli isolates from lesion-bearing animal organs. This study investigated the genetic characteristics of chromosome-mediated mcr-1 and plasmid-mediated blaNDM-5 in E. coli isolated from lesion-bearing animal organs. Nine mcr-1- and blaNDM-5-positive E. coli strains (MNPECs) showed extensive drug resistance (XDR). The predominant clonal complexes (CC) mainly belonged to CC156, CC10, and CC165 from the 56 MNEPCs (including nine strains in this study) retrieved from the literature. These strains were widely distributed in China, and originated from pig fecal samples, human stool/urine samples as well as intestinal contents of chicken. Two transconjugants harboring blaNDM-5 gene were also successfully obtained from two donors (J-8 and N-14) and this transfer increased the MIC for meropenem by 256 times. However, conjugative transfer of mcr-1 gene failed. Both J-8 and N-14 strains contained point mutations associated with quinolone resistance and more than three types of AMR genes, including the mcr-1 gene on the chromosome and the blaNDM-5 gene on the IncX3-type plasmid. The genetic structure of mcr-1 located on the chromosome was an intact Tn6330, and blaNDM-5-carrying IncX3-type plasmid was ISAb125-IS5-blaNDM-5-bleO-trpF-tat-cutA-IS26 gene cassette. Moreover, differences between chromosomes included additional partial sequence of phage integrated into host genome and the different genes associated with O-antigen synthesis.
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Affiliation(s)
- Yungai Xiang
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zengyuan Liu
- College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Guo Yu
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuxia Song
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Li
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xujing Geng
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Liying Ma
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Junqing Guo
- Henan Institute of Modern Chinese Veterinary Medicine, Zhengzhou, Henan, China
| | - Li Tan
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Li Tan,
| | - Pengju Chen
- Henan Institute of Modern Chinese Veterinary Medicine, Zhengzhou, Henan, China
- Shandong Xindehui Biotechnology Company Ltd., Yuncheng, Shandong, China
- Pengju Chen,
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