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Leong LE, Coldbeck-Shackley RC, McMillan M, Bratcher HB, Turra M, Lawrence A, Kahler C, Maiden MC, Rogers GB, Marshall H. The genomic epidemiology of Neisseria meningitidis carriage from a randomised controlled trial of 4CMenB vaccination in an asymptomatic adolescent population. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2024; 43:100966. [PMID: 38169944 PMCID: PMC10758868 DOI: 10.1016/j.lanwpc.2023.100966] [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: 07/27/2023] [Revised: 10/18/2023] [Accepted: 11/01/2023] [Indexed: 01/05/2024]
Abstract
Background Oropharyngeal carriage of Neisseria meningitidis is frequent during adolescence, representing a major source of invasive meningococcal disease. This study examined the impact of a serogroup B vaccination (Bexsero, GSK 4CMenB) programme on adolescent N. meningitidis carriage using genomic data. Methods A total 34,489 oropharyngeal samples were collected as part of a state-wide cluster randomised-controlled trial in South Australia during 2017 and 2018 (NCT03089086). Samples were screened for the presence of N. meningitidis DNA by porA PCR prior to culture. Whole genome sequencing was performed on all 1772 N. meningitidis culture isolates and their genomes were analysed. Findings Unencapsulated meningococci were predominant at baseline (36.3% of isolates), followed by MenB (31.0%), and MenY (20.5%). Most MenB were ST-6058 from hyperinvasive cc41/44, or ST-32 and ST-2870 from cc32. For MenY, ST-23 and ST-1655 from cc23 were prevalent. Meningococcal carriage was mostly unchanged due to the vaccination programme; however, a significant reduction in ST-53 capsule-null meningococci prevalence was observed in 2018 compared to 2017 (OR = 0.52; 95% CI: 0.30-0.87, p = 0.0106). This effect was larger in the vaccinated compared to the control group (OR = 0.37; 95% CI: 0.12-0.98, p = 0.0368). Interpretation While deployment of the 4CMenB vaccination did not alter the carriage of hyperinvasive MenB in the vaccinated population, it altered the carriage of other N. meningitidis sequence types following the vaccination program. Our findings suggest 4CMenB vaccination is unlikely to reduce transmission of hyperinvasive N. meningitidis strains and therefore ongoing targeted vaccination is likely a more effective public health intervention. Funding This work was funded by GlaxoSmithKline Biologicals SA.
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Affiliation(s)
- Lex E.X. Leong
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia
- Microbiome & Host Health, South Australian Health and Medical Research Institute, Bedford Park, 5042, Australia
| | | | - Mark McMillan
- Vaccinology and Immunology Research Trials Unit, Women’s and Children’s Health Network, Adelaide 5000, Australia
- Robinson Research Institute and Adelaide Medical School, The University of Adelaide, Adelaide 5000, Australia
| | - Holly B. Bratcher
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, United Kingdom
| | - Mark Turra
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000, Australia
| | - Andrew Lawrence
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000, Australia
| | | | - Martin C.J. Maiden
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, United Kingdom
| | - Geraint B. Rogers
- Microbiome & Host Health, South Australian Health and Medical Research Institute, Bedford Park, 5042, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, 5042, Australia
| | - Helen Marshall
- Vaccinology and Immunology Research Trials Unit, Women’s and Children’s Health Network, Adelaide 5000, Australia
- Robinson Research Institute and Adelaide Medical School, The University of Adelaide, Adelaide 5000, Australia
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Aguirre-Sanchez JR, Vega-Lopez IF, Castro Del Campo N, Medrano-Felix JA, Martínez-Urtaza J, Chaidez-Quiroz C. Genomic-wide analysis approach revealed genomic similarity for environmental Mexican S. Oranienburg genomes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024; 34:956-967. [PMID: 36946386 DOI: 10.1080/09603123.2023.2191312] [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: 01/09/2023] [Accepted: 03/12/2023] [Indexed: 06/18/2023]
Abstract
As the human population grows, an increase in food trade is needed. This elevates the risk of epidemiological outbreaks. One of the prevalent pathogens associated with food production in Mexico has been Salmonella Oranienburg. Effective surveillance systems require microbial genetic knowledge. The objective of this work is to describe the genetic composition of Mexican S. Oranienburg genomes. For that, 53 strains from different environmental sources were isolated and sequenced. Additionally, 109 S. Oranienburg genomes were downloaded. Bioinformatic analyses were used to explore the clonal complex and genomic relatedness. A major clonal group formed by ST23 was identified comprising four STs. 202 SNPs were found the maximum difference among isolates. Virulence genes for host invasion and colonization as rpoS, fimbria type 1, and, T3SS were found common for all isolates. This study suggests that Mexican S. Oranienburg strains are potential pathogens circulating continuously in the region between host and non-host environments.
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Affiliation(s)
- J R Aguirre-Sanchez
- Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo, Culiacán, México
| | - I F Vega-Lopez
- Laboratorio en Ciencia y Mineria de Datos, Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacán, México
| | - N Castro Del Campo
- Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo, Culiacán, México
| | - J A Medrano-Felix
- Inocuidad Alimentaria, Investigadoras e Investigadores por México-Centro de Investigación en Alimentación y Desarrollo A.C, Culiacán, México
| | - J Martínez-Urtaza
- Departement of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - C Chaidez-Quiroz
- Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo, Culiacán, México
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203
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Telhig S, Pham NP, Ben Said L, Rebuffat S, Ouellette M, Zirah S, Fliss I. Exploring the genetic basis of natural resistance to microcins. Microb Genom 2024; 10:001156. [PMID: 38407259 PMCID: PMC10926693 DOI: 10.1099/mgen.0.001156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 11/28/2023] [Indexed: 02/27/2024] Open
Abstract
Enterobacteriaceae produce an arsenal of antimicrobial compounds including microcins, ribosomally produced antimicrobial peptides showing diverse structures and mechanisms of action. Microcins target close relatives of the producing strain to promote its survival. Their narrow spectrum of antibacterial activity makes them a promising alternative to conventional antibiotics, as it should decrease the probability of resistance dissemination and collateral damage to the host's microbiota. To assess the therapeutic potential of microcins, there is a need to understand the mechanisms of resistance to these molecules. In this study, we performed genomic analyses of the resistance to four microcins [microcin C, a nucleotide peptide; microcin J25, a lasso peptide; microcin B17, a linear azol(in)e-containing peptide; and microcin E492, a siderophore peptide] on a collection of 54 Enterobacteriaceae from three species: Escherichia coli, Salmonella enterica and Klebsiella pneumoniae. A gene-targeted analysis revealed that about half of the microcin-resistant strains presented mutations of genes involved in the microcin mechanism of action, especially those involved in their uptake (fhuA, fepA, cirA and ompF). A genome-wide association study did not reveal any significant correlations, yet relevant genetic elements were associated with microcin resistance. These were involved in stress responses, biofilm formation, transport systems and acquisition of immunity genes. Additionally, microcin-resistant strains exhibited several mutations within genes involved in specific metabolic pathways, especially for S. enterica and K. pneumoniae.
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Affiliation(s)
- Soufiane Telhig
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Nguyen Phuong Pham
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Laila Ben Said
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Ismaïl Fliss
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
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Stepanić M, Duvnjak S, Reil I, Hađina S, Kempf VAJ, Špičić S, Mihaljević Ž, Beck R. Epidemiology of Bartonella henselae infection in pet and stray cats in Croatia with risk factors analysis. Parasit Vectors 2024; 17:48. [PMID: 38303085 PMCID: PMC10832190 DOI: 10.1186/s13071-024-06117-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Cats are the primary reservoirs of the bacterium Bartonella henselae, the main cause of cat-scratch disease in humans. The main vector of the bacterium is the cat flea, Ctenocephalides felis. In southeastern Europe, data are lacking on the prevalence of B. henselae infection in cats, the strains of B. henselae involved and the risk factors associated with the infection. METHODS Blood samples collected in ethylenediaminetetraacetic acid-containing tubes from 189 domestic cats (156 pet cats and 33 stray cats) from Zagreb, the capital city of Croatia, and 10 counties throughout Croatia were cultured for Bartonella spp. Following culture, bacterial isolates were genotyped at eight loci after using PCR to amplify 16S ribosomal RNA (rRNA) and the internal transcribed spacer region between the 16S and 23S rRNA sequences. Univariate and multivariate logistic regression were used to identify risk factors for B. henselae infection in cats. RESULTS Bartonella spp. was detected in 31 cats (16.4%), and subsequent genotyping at the eight loci revealed B. henselae in all cases. Thirty complete multilocus sequence typing profiles were obtained, and the strains were identified as four sequence types that had been previously reported, namely ST5 (56.7%), ST6 (23.3%), ST1 (13.3%) and ST24 (3.3%), as well as a novel sequence type, ST33 (3.3%). The univariate analysis revealed a significantly higher risk of B. henselae infection in cats residing in coastal areas of Croatia (odds ratio [OR] 2.592, 95% confidence interval [CI] 1.150-5.838; P = 0.0191) and in cats with intestinal parasites (OR 3.207, 95% CI 1.088-9.457; P = 0.0279); a significantly lower risk was identified in cats aged > 1 year (OR 0.356, 95% CI 0.161-0.787; P = 0.0247) and in cats sampled between April and September (OR 0.325, 95% CI 0.147-0.715; P = 0.005). The multivariate analysis that controlled for age showed a positive association with the presence of intestinal parasites (OR 4.241, 95% CI 1.243-14.470; P = 0.0119) and coastal residence (OR 2.567, 95% CI 1.114-5.915; P = 0.0216) implying increased risk of infection, and a negative association with sampling between April and September (OR 0.379, 95% CI 0.169-0.848; P = 0.018) implying a decreased risk of infection. After controlling for the season, an increased risk of infection remained for the coastal region (OR 2.725, 95% CI 1.200-6.186; P = 0.012). CONCLUSIONS Bartonella henselae is prevalent throughout Croatia and is a public health threat. Environmental and host factors can significantly affect the risk of infection, and these should be explored in more detail. The presence of intestinal parasites highlights the need to eliminate the flea vector, Ctenocephalides felis, as the most effective approach to control infections in cats and humans.
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Affiliation(s)
- Maja Stepanić
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, Savska Cesta 143, 10000, Zagreb, Croatia.
| | - Sanja Duvnjak
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, Savska Cesta 143, 10000, Zagreb, Croatia
| | - Irena Reil
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, Savska Cesta 143, 10000, Zagreb, Croatia
| | - Suzana Hađina
- Department of Microbiology and Infectious Diseases, with Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000, Zagreb, Croatia
| | - Volkhard A J Kempf
- Institute for Medical Microbiology and Hospital Hygiene and Consulting Laboratory for Bartonella Infections, University Hospital Frankfurt, Paul-Ehrlich-Straße 40, 60596, Frankfurt, Germany
| | - Silvio Špičić
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, Savska Cesta 143, 10000, Zagreb, Croatia
| | - Željko Mihaljević
- Department of Pathology, Croatian Veterinary Institute, Savska Cesta 143, 10000, Zagreb, Croatia
| | - Relja Beck
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, Savska Cesta 143, 10000, Zagreb, Croatia.
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205
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Unitt A, Maiden M, Harrison O. Characterizing the diversity and commensal origins of penA mosaicism in the genus Neisseria. Microb Genom 2024; 10:001209. [PMID: 38381035 PMCID: PMC10926701 DOI: 10.1099/mgen.0.001209] [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: 01/03/2024] [Accepted: 02/10/2024] [Indexed: 02/22/2024] Open
Abstract
Mosaic penA alleles formed through horizontal gene transfer (HGT) have been instrumental to the rising incidence of ceftriaxone-resistant gonococcal infections. Although interspecies HGT of regions of the penA gene between Neisseria gonorrhoeae and commensal Neisseria species has been described, knowledge concerning which species are the most common contributors to mosaic penA alleles is limited, with most studies examining only a small number of alleles. Here, we investigated the origins of recombinant penA alleles through in silico analyses that incorporated 1700 penA alleles from 35 513 Neisseria isolates, comprising 15 different Neisseria species. We identified Neisseria subflava and Neisseria cinerea as the most common source of recombinant sequences in N. gonorrhoeae penA. This contrasted with Neisseria meningitidis penA, for which the primary source of recombinant DNA was other meningococci, followed by Neisseria lactamica. Additionally, we described the distribution of polymorphisms implicated in antimicrobial resistance in penA, and found that these are present across the genus. These results provide insight into resistance-related changes in the penA gene across human-associated Neisseria species, illustrating the importance of genomic surveillance of not only the pathogenic Neisseria, but also of the oral niche-associated commensals from which these pathogens are sourcing key genetic variation.
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Affiliation(s)
- Anastasia Unitt
- Department of Biology, University of Oxford, Oxford, OX1 3SY, UK
| | - Martin Maiden
- Department of Biology, University of Oxford, Oxford, OX1 3SY, UK
| | - Odile Harrison
- Department of Biology, University of Oxford, Oxford, OX1 3SY, UK
- Infectious Disease Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, OX3 7LF, UK
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206
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Anbazhagan S, Himani KM, Karthikeyan R, Prakasan L, Dinesh M, Nair SS, Lalsiamthara J, Abhishek, Ramachandra SG, Chaturvedi VK, Chaudhuri P, Thomas P. Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains. Int Microbiol 2024; 27:101-111. [PMID: 37202587 DOI: 10.1007/s10123-023-00374-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: 01/31/2023] [Revised: 04/29/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Brucella abortus and Brucella melitensis are the primary etiological agents of brucellosis in large and small ruminants, respectively. There are limited comparative genomic studies involving Brucella strains that explore the relatedness among both species. In this study, we involved strains (n=44) representing standard, vaccine and Indian field origin for pangenome, single nucleotide polymorphism (SNP) and phylogenetic analysis. Both species shared a common gene pool representing 2884 genes out of a total 3244 genes. SNP-based phylogenetic analysis indicated higher SNP diversity among B. melitensis (3824) strains in comparison to B. abortus (540) strains, and a clear demarcation was identified between standard/vaccine and field strains. The analysis for virulence genes revealed that virB3, virB7, ricA, virB5, ipx5, wbkC, wbkB, and acpXL genes were highly conserved in most of the Brucella strains. Interestingly, virB10 gene was found to have high variability among the B. abortus strains. The cgMLST analysis revealed distinct sequence types for the standard/vaccine and field strains. B. abortus strains from north-eastern India fall within similar sequence type differing from other strains. In conclusion, the analysis revealed a highly shared core genome among two Brucella species. SNP analysis revealed B. melitensis strains exhibit high diversity as compared to B. abortus strains. Strains with absence or high polymorphism of virulence genes can be exploited for the development of novel vaccine candidates effective against both B. abortus and B. melitensis.
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Affiliation(s)
- S Anbazhagan
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
- ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, India
| | - K M Himani
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - R Karthikeyan
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Lakshmi Prakasan
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - M Dinesh
- Division of Pathology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Sonu S Nair
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Jonathan Lalsiamthara
- Department of Molecular Microbiology & Immunology, SOM, OHSU, Portland, OR, US, 97239, USA
| | - Abhishek
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - S G Ramachandra
- ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, India
| | - V K Chaturvedi
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Pallab Chaudhuri
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India.
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India.
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207
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Raghuram V, Petit RA, Karol Z, Mehta R, Weissman DB, Read TD. Average Nucleotide Identity based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577756. [PMID: 38352482 PMCID: PMC10862745 DOI: 10.1101/2024.01.29.577756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Staphylococcus aureus causes both hospital and community acquired infections in humans worldwide. Due to the high incidence of infection S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public S. aureus Illumina whole genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains. Pairwise comparison of core gene Average Nucleotide Identity (ANI) revealed a natural boundary of 99.5% that could be used to define 145 distinct strains within the species. We found that intermediate frequency genes in the pangenome (present in 10-95% of genomes) could be divided into those closely linked to strain background ("strain-concentrated") and those highly variable within strains ("strain-diffuse"). Non-core genes had different patterns of chromosome location; notably, strain-diffuse associated with prophages, strain-concentrated with the vSaβ genome island and rare genes (<10% frequency) concentrated near the origin of replication. Antibiotic genes were enriched in the strain-diffuse class, while virulence genes were distributed between strain-diffuse, strain-concentrated, core and rare classes. This study shows how different patterns of gene movement help create strains as distinct subspecies entities and provide insight into the diverse histories of important S. aureus functions.
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Affiliation(s)
- Vishnu Raghuram
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Robert A Petit
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Zach Karol
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | - Rohan Mehta
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | | | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
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208
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Jünger C, Imkamp F, Balakrishna S, Gysin M, Haldimann K, Brugger SD, Scheier TC, Hampel B, Hobbie SN, Günthard HF, Braun DL. Phenotypic and genotypic characterization of Neisseria gonorrhoeae isolates among individuals at high risk for sexually transmitted diseases in Zurich, Switzerland. Int J STD AIDS 2024:9564624241230266. [PMID: 38297880 DOI: 10.1177/09564624241230266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
BACKGROUND While ceftriaxone resistance remains scarce in Switzerland, global Neisseria gonorrhoeae (NG) antimicrobial resistance poses an urgent threat. This study describes clinical characteristics in MSM (men who have sex with men) diagnosed with NG infection and analyses NG resistance by phenotypic and genotypic means. METHODS Data of MSM enrolled in three clinical cohorts with a positive polymerase chain reaction test (PCR) for NG were analysed between January 2019 and December 2021 and linked with antibiotic susceptibility testing. Bacterial isolates were subjected to whole genome sequencing (WGS). RESULTS Of 142 participants, 141 (99%) were MSM and 118 (84%) living with HIV. Participants were treated with ceftriaxone (N = 79), azithromycin (N = 2), or a combination of both (N = 61). No clinical or microbiological failures were observed. From 182 positive PCR samples taken, 23 were available for detailed analysis. Based on minimal inhibitory concentrations (MICs), all isolates were susceptible to ceftriaxone, gentamicin, cefixime, cefpodoxime, ertapenem, zoliflodacin, and spectinomycin. Resistance to azithromycin, tetracyclines and ciprofloxacin was observed in 10 (43%), 23 (100%) and 11 (48%) of the cases, respectively. Analysis of WGS data revealed combinations of resistance determinants that matched with the corresponding phenotypic resistance pattern of each isolate. CONCLUSION Among the MSM diagnosed with NG mainly acquired in Switzerland, ceftriaxone MICs were low for a subset of bacterial isolates studied and no treatment failures were observed. For azithromycin, high occurrences of in vitro resistance were found. Gentamicin, cefixime, cefpodoxime, ertapenem, spectinomycin, and zoliflodacin displayed excellent in vitro activity against the 23 isolates underscoring their potential as alternative agents to ceftriaxone.
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Affiliation(s)
- Christian Jünger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Suraj Balakrishna
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marina Gysin
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Klara Haldimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas C Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Sven N Hobbie
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Dominique L Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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209
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Stracquadanio S, Nicolosi A, Privitera GF, Massimino M, Marino A, Bongiorno D, Stefani S. Role of transcriptomic and genomic analyses in improving the comprehension of cefiderocol activity in Acinetobacter baumannii. mSphere 2024; 9:e0061723. [PMID: 38078714 PMCID: PMC10826366 DOI: 10.1128/msphere.00617-23] [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: 10/18/2023] [Accepted: 11/05/2023] [Indexed: 01/31/2024] Open
Abstract
The mechanisms of action and resistance of cefiderocol (FDC) in Acinetobacter baumannii are still not fully elucidated, but iron transport systems have been evoked in its entry into the cell to reach the penicillin-binding proteins (PBPs). To capture the dynamics of gene expression related to FDC action in various conditions, we report on the genomic and transcriptomic features of seven A. baumannii strains with different FDC susceptibility, focusing on the variants in genes associated with β-lactam resistance and the expression of the siderophore biosynthesis and transport systems acinetobactin and baumannoferrin. We also investigated the expression of the TonB energy transduction system (ETS) and siderophore receptors piuA and pirA. The four clinical samples belonged to the same clonal complex (CC2), and the two strains with the highest FDC MICs showed peculiar variants in PBP2 and ampC. Similarly, the two clinical strains with the lowest MICs shared variants in an outer membrane protein as well as ampC. Gene expression analyses highlighted the up-regulation of the acinetobactin and baumannoferrin genes in response to iron depletion and a down-regulation in the presence of high iron concentrations. In response to FDC, gene expression seemed strain-dependent, probably due to the different metabolic features of each strain. Overall, FDC activates the ETS, confirming the active import of the drug; baumannoferrin, more than acinetobactin, appeared stimulated by FDC in an iron-depleted medium. In conclusion, iron transport systems play a clear role in the FDC uptake, and their expression likely contributes to MIC variation together with β-lactam resistance determinants.IMPORTANCEAcinetobacter baumannii poses a threat to healthcare due to its ability to give difficult-to-treat infections as a consequence of our shortage of antibiotic molecules active on this multidrug-resistant bacterium. Cefiderocol (FDC) represents one of the few drugs active on A. baumannii, and to preserve its activity, this study explored the transcriptomic and genomic features of seven strains with varying susceptibility to FDC. Transcriptomic analyses revealed the different effects of FDC on iron transport systems, promoting mainly baumannoferrin expression-thus more likely related to FDC entry-and the energy transduction systems. These findings suggest that not all iron transport systems are equally involved in FDC entry into A. baumannii cells. Finally, mutations in PBPs and β-lactamases may contribute to the resistance onset. Overall, the study sheds light on the importance of iron availability and metabolic differences in FDC resistance, offering insights into understanding the evolution of resistance in A. baumannii strains.
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Affiliation(s)
- Stefano Stracquadanio
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, Catania, Italy
| | - Alice Nicolosi
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, Catania, Italy
| | - Grete Francesca Privitera
- Department of Clinical and Experimental Medicine, Unit of Math and Comp Science, University of Catania, Catania, Italy
| | - Mariacristina Massimino
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Andrea Marino
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, Catania, Italy
| | - Dafne Bongiorno
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, Catania, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, Catania, Italy
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Flores-Oropeza MA, Ochoa SA, Cruz-Córdova A, Chavez-Tepecano R, Martínez-Peñafiel E, Rembao-Bojórquez D, Zavala-Vega S, Hernández-Castro R, Flores-Encarnacion M, Arellano-Galindo J, Vélez D, Xicohtencatl-Cortes J. Comparative genomic analysis of uropathogenic Escherichia coli strains from women with recurrent urinary tract infection. Front Microbiol 2024; 14:1340427. [PMID: 38328583 PMCID: PMC10848155 DOI: 10.3389/fmicb.2023.1340427] [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: 11/17/2023] [Accepted: 12/21/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction Recurrent urinary tract infections (RUTIs) caused by uropathogenic Escherichia coli are costly public health problems impacting patients' quality of life. Aim In this work, a comparative genomics analysis of three clinical RUTI strains isolated from bladder biopsy specimens was performed. Materials and methods One hundred seventy-two whole genomes of urinary tract E. coli strains were selected from the NCBI database. The search for virulence factors, fitness genes, regions of interest, and genetic elements associated with resistance was manually carried out. The phenotypic characterization of antibiotic resistance, haemolysis, motility, and biofilm formation was performed. Moreover, adherence and invasion assays with human bladder HTB-5 cells, and transmission electron microscopy (TEM) were performed. Results The UTI-1_774U and UTI-3_455U/ST1193 strains were associated with the extraintestinal pathotypes, and the UTI-2_245U/ST295 strain was associated with the intestinal pathotype, according to a phylogenetic analysis of 172 E. coli urinary strains. The three RUTI strains were of clinical, epidemiological, and zoonotic relevance. Several resistance genes were found within the plasmids of these strains, and a multidrug resistance phenotype was revealed. Other virulence genes associated with CFT073 were not identified in the three RUTI strains (genes for type 1 and P fimbriae, haemolysin hlyA, and sat toxin). Quantitative adherence analysis showed that UTI-1_774U was significantly (p < 0.0001) more adherent to human bladder HTB-5 cells. Quantitative invasion analysis showed that UTI-2_245U was significantly more invasive than the control strains. No haemolysis or biofilm activity was detected in the three RUTI strains. The TEM micrographs showed the presence of short and thin fimbriae only in the UTI-2_245U strain. Conclusion The high variability and genetic diversity of the RUTI strains indicate that are a mosaic of virulence, resistance, and fitness genes that could promote recurrence in susceptible patients.
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Affiliation(s)
- Marco A. Flores-Oropeza
- Posgrado en Ciencias Biomédicas, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Sara A. Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - Eva Martínez-Peñafiel
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Daniel Rembao-Bojórquez
- Departamento de Patología, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Mexico City, Mexico
| | - Sergio Zavala-Vega
- Departamento de Patología, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Mexico City, Mexico
- Laboratorio Clínico y Banco de Sangre, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Mexico City, Mexico
| | - Rigoberto Hernández-Castro
- Departmento de Ecología de Agentes Patógenos, Hospital General “Dr. Manuel Gea González”, Mexico City, Mexico
| | - Marcos Flores-Encarnacion
- Laboratorio de Microbiología Molecular y Celular, Biomedicina, Facultad de Medicina, BUAP, Puebla, Mexico
| | - José Arellano-Galindo
- Laboratorio de Virología Clínica y Experimental, Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Daniel Vélez
- Hospital Militar de Especialidades de la Mujer y Neonatología, Mexico City, Mexico
- Unidad Médica de Alta Especialidad, Hospital de Ginecología y Obstetricia No. 3 IMSS, Mexico City, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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Yoshida H, Takayama Y, Goto M, Maeda T, Tsuyuki Y, Takahashi T. Human Keratinocyte Entry of Noninvasive Streptococcus dysgalactiae Subsp. equisimilis from Humans and Companion Animals: Relatedness with Lancefield Group, Source, Virulence-Associated Genes, and Antimicrobial Resistance Phenotype. Jpn J Infect Dis 2024; 77:25-33. [PMID: 37779027 DOI: 10.7883/yoken.jjid.2023.310] [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: 10/03/2023]
Abstract
We evaluated the cell invasion ability (CIA) of non-invasive Streptococcus dysgalactiae subsp. equisimilis using human keratinocytes and determined the association of CIA populations with their hosts and microbiological traits. Forty-two isolates from humans and companion animals were selected with host information. In addition to CIA, virulence-associated gene (VAG, spegg-ska-scpA-inlA-sicG-brpA-prtF1-prtF2-lmb-cbp-srtp1-srtp2) profiling, emm genotyping, multilocus sequence typing, and antimicrobial resistance (AMR) phenotyping/genotyping were performed. We designated CIA values higher than the mean of all isolates as high-frequency and those lower than the mean as low-frequency. Differences in the CIA between the different sources and Lancefield groups were assessed. We analyzed the association between high- and low-frequency CIA and VAG, emm genotype, sequence type/clonal complex, and AMR phenotype/genotype. Based on the mean (19.368 colony-forming units/100 cells) of 42 isolates, eight isolates had high-frequency CIA, whereas 34 had low-frequency CIA. We found an association between low-frequency CIA population and group G isolates, as well as a link between high-frequency CIA population and group C isolates. We also observed associations between low-frequency CIA population and oral/respiratory tract origin, ska, scpA, and lmb detection, and the AMR phenotype. Our observations suggest potential associations between high-/low-frequency CIA and the group, source, VAG, and AMR phenotypes.
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Affiliation(s)
- Haruno Yoshida
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Japan
| | - Yoshiko Takayama
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Japan
- Division of Clinical Laboratory, Byotai-Seiri Laboratory, Japan
| | - Mieko Goto
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Japan
| | - Takahiro Maeda
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Japan
| | - Yuzo Tsuyuki
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Japan
- Division of Clinical Laboratory, Sanritsu Zelkova Veterinary Laboratory, Japan
| | - Takashi Takahashi
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Japan
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212
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Niu C, Song X, Hao J, Zhao M, Yuan Y, Liu J, Yue T. Identification of Burkholderia gladioli pv. cocovenenans in Black Fungus and Efficient Recognition of Bongkrekic Acid and Toxoflavin Producing Phenotype by Back Propagation Neural Network. Foods 2024; 13:351. [PMID: 38275718 PMCID: PMC10815087 DOI: 10.3390/foods13020351] [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: 12/18/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Burkholderia gladioli pv. cocovenenans is a serious safety issue in black fungus due to the deadly toxin, bongkrekic acid. This has triggered the demand for an efficient toxigenic phenotype recognition method. The objective of this study is to develop an efficient method for the recognition of toxin-producing B. gladioli strains. The potential of multilocus sequence typing and a back propagation neural network for the recognition of toxigenic B. cocovenenans was explored for the first time. The virulent strains were isolated from a black fungus cultivation environment in Qinba Mountain area, Shaanxi, China. A comprehensive evaluation of toxigenic capability of 26 isolates were conducted using Ultra Performance Liquid Chromatography for determination of bongkrekic acid and toxoflavin production in different culturing conditions and foods. The isolates produced bongkrekic acid in the range of 0.05-6.24 mg/L in black fungus and a highly toxin-producing strain generated 201.86 mg/L bongkrekic acid and 45.26 mg/L toxoflavin in co-cultivation with Rhizopus oryzae on PDA medium. Multilocus sequence typing phylogeny (MLST) analysis showed that housekeeping gene sequences have a certain relationship with a strain toxigenic phenotype. We developed a well-trained, back-propagation neutral network for prediction of toxigenic phenotype in B. gladioli based on MLST sequences with an accuracy of 100% in the training set and an accuracy of 86.7% in external test set strains. The BP neutral network offers a highly efficient approach to predict toxigenic phenotype of strains and contributes to hazard detection and safety surveillance.
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Affiliation(s)
- Chen Niu
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (C.N.); (X.S.); (J.H.); (Y.Y.)
| | - Xiying Song
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (C.N.); (X.S.); (J.H.); (Y.Y.)
| | - Jin Hao
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (C.N.); (X.S.); (J.H.); (Y.Y.)
| | - Mincheng Zhao
- The 20th Research Institute of CETC, Xi’an 710068, China
| | - Yahong Yuan
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (C.N.); (X.S.); (J.H.); (Y.Y.)
| | - Jingyan Liu
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (C.N.); (X.S.); (J.H.); (Y.Y.)
| | - Tianli Yue
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (C.N.); (X.S.); (J.H.); (Y.Y.)
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213
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Hem S, Cummins ML, Wyrsch ER, Drigo B, Hoye BJ, Maute K, Sanderson-Smith M, Gorman J, Bogema DR, Jenkins C, Deutscher AT, Yam J, Hai F, Donner E, Jarocki VM, Djordjevic SP. Genomic analysis of Citrobacter from Australian wastewater and silver gulls reveals novel sequence types carrying critically important antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168608. [PMID: 37977387 DOI: 10.1016/j.scitotenv.2023.168608] [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: 08/17/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Antimicrobial resistance (AMR) is a major public health concern, and environmental bacteria have been recognized as important reservoirs of antimicrobial resistance genes (ARGs). Citrobacter, a common environmental bacterium and opportunistic pathogen in humans and other animals, has been largely understudied in terms of its diversity and AMR potential. Whole-genome (short-read) sequencing on a total of 77 Citrobacter isolates obtained from Australian silver gull (Chroicocephalus novaehollandiae) (n = 17) and influent wastewater samples (n = 60) was performed, revealing a diverse Citrobacter population, with seven different species and 33 sequence types, 17 of which were novel. From silver gull using non-selective media we isolated a broader range of species with little to no mobilised ARG carriage. Wastewater isolates (selected using Carbapenem- Resistant Enterobacterales (CRE) selective media) carried a heavy burden of ARGs (up to 21 ARGs, conferring resistance to nine classes of antibiotics), with several novel multidrug-resistant (MDR) lineages identified, including C. braakii ST1110, which carried ARGs conferring resistance to eight to nine classes of antibiotics, and C. freundii ST1105, which carried two carbapenemase genes, blaIMP-4 in class 1 integron structure, and blaKPC-2. Additionally, we identified an MDR C. portucalensis isolate carrying blaNDM-1, blaSHV-12, and mcr-9. We identified IncC, IncM2, and IncP6 plasmids as the likely vectors for many of the critically important mobilised ARGs. Phylogenetic analyses were performed to assess any epidemiological linkages between isolation sources, demonstrating low relatedness across sources beyond the ST level. However, these analyses did reveal some closer relationships between strains from disparate wastewater sources despite their collection some 13,000 km apart. These findings support the need for future surveillance of Citrobacter populations in wastewater and wildlife populations to monitor for potential opportunistic human pathogens.
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Affiliation(s)
- Sopheak Hem
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Barbara Drigo
- UniSA STEM, University of South Australia, Adelaide, SA, Australia
| | - Bethany J Hoye
- School of Earth, Atmospheric and Life Sciences, University of Wollongong NSW, Australia; Environmental Futures Research Centre, University of Wollongong NSW, Australia
| | - Kimberly Maute
- School of Earth, Atmospheric and Life Sciences, University of Wollongong NSW, Australia; Environmental Futures Research Centre, University of Wollongong NSW, Australia
| | - Martina Sanderson-Smith
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, NSW, Australia
| | - Jody Gorman
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, NSW, Australia
| | - Daniel R Bogema
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Cheryl Jenkins
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Ania T Deutscher
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Jerald Yam
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Faisal Hai
- School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, NSW, Australia
| | - Erica Donner
- Cooperative Research Centre for Solving Antimicrobial resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia; Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia.
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia.
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214
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Wan Y, Myall AC, Boonyasiri A, Bolt F, Ledda A, Mookerjee S, Weiße AY, Getino M, Turton JF, Abbas H, Prakapaite R, Sabnis A, Abdolrasouli A, Malpartida-Cardenas K, Miglietta L, Donaldson H, Gilchrist M, Hopkins KL, Ellington MJ, Otter JA, Larrouy-Maumus G, Edwards AM, Rodriguez-Manzano J, Didelot X, Barahona M, Holmes AH, Jauneikaite E, Davies F. Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes. J Infect Dis 2024:jiae019. [PMID: 38245822 DOI: 10.1093/infdis/jiae019] [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: 09/19/2023] [Revised: 01/02/2024] [Accepted: 01/19/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of IMP-encoding CPE amongst diverse Enterobacterales species between 2016 and 2019 across a London regional network. METHODS We performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE positive patients. Genomes of IMP-encoding CPE isolates were overlayed with patient contacts to imply potential transmission events. RESULTS Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, E. coli); 86% (72/84) harboured an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68/72). Phylogenetic analysis of IncHI2 plasmids identified three lineages showing significant association with patient contacts and movements between four hospital sites and across medical specialities, which was missed on initial investigations. CONCLUSIONS Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multi-modal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.
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Affiliation(s)
- Yu Wan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ashleigh C Myall
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Frances Bolt
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
- Centre for Antimicrobial Optimisation, Hammersmith Hospital, Imperial College London, Du Cane Road, London, United Kingdom
| | - Alice Ledda
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, United Kingdom
| | | | - Andrea Y Weiße
- School of Biological Sciences, University of Edinburgh, Scotland, United Kingdom
- School of Informatics, University of Edinburgh, Scotland, United Kingdom
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jane F Turton
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, United Kingdom
| | - Hala Abbas
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Microbiology, North West London Pathology, London, United Kingdom
| | - Ruta Prakapaite
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Akshay Sabnis
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | | | - Kenny Malpartida-Cardenas
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, United Kingdom
| | - Luca Miglietta
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, United Kingdom
| | - Hugo Donaldson
- Department of Microbiology, North West London Pathology, London, United Kingdom
| | - Mark Gilchrist
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Katie L Hopkins
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, United Kingdom
| | - Matthew J Ellington
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Reference Services Division, UK Health Security Agency, London, United Kingdom
| | - Jonathan A Otter
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Gerald Larrouy-Maumus
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Andrew M Edwards
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jesus Rodriguez-Manzano
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Centre for Antimicrobial Optimisation, Hammersmith Hospital, Imperial College London, Du Cane Road, London, United Kingdom
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, United Kingdom
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, United Kingdom
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Alison H Holmes
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
- Centre for Antimicrobial Optimisation, Hammersmith Hospital, Imperial College London, Du Cane Road, London, United Kingdom
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Frances Davies
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
- Department of Microbiology, North West London Pathology, London, United Kingdom
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Guitart-Matas J, Espunyes J, Illera L, Gonzalez-Escalona N, Ribas MP, Marco I, Migura-Garcia L. High-risk lineages of extended spectrum cephalosporinase producing Escherichia coli from Eurasian griffon vultures (Gyps fulvus) foraging in landfills in north-eastern Spain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168625. [PMID: 37977396 DOI: 10.1016/j.scitotenv.2023.168625] [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: 09/21/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Extended-spectrum cephalosporinase producing (ESC) E. coli are regarded as key indicator microorganisms of antimicrobial resistance (AMR), calling for a One Health integrated global surveillance strategy. Wildlife is exposed to antibiotic contaminants and/or resistant bacteria that have been released into the environment, potentially acting as reservoirs and spreaders of resistance genes as well as sentinels of anthropogenic pressure. Monitoring AMR in wildlife has become crucial in determining anthropogenic environmental impacts as well as transmission routes. In this study, we determined the occurrence and potential sources of ESC E. coli in 218 Eurasian griffon vultures (Gyps fulvus) foraging regularly on human waste disposed at a dumpsite in north-eastern Spain. Minimal inhibitory concentration for 14 different antimicrobials was performed to evaluate the phenotype of the isolates, and whole genome sequencing was carried out to investigate lineages and plasmids harbouring ESC genes. Our sequences were compared to previously published Spanish sequences of human, animal, and wildlife origin. We report a high prevalence of CTX-M-15, as well as the presence of other resistance genes such as OXA-10, CTX-M-27, and CTX-M-65 which are rarely described in European livestock, suggesting a human origin. The isolates also carried a diverse range of additional AMR genes for a broad spectrum of drug families, with the majority being multi-drug resistant. The phylogenomic analyses suggests the transmission of high-risk lineages from humans to vultures, with 49 % of our isolates matching the most common extraintestinal pathogenic E. coli (ExPEC) lineages described in humans worldwide, including ST131, ST10 and ST58. We conclude that anthropogenically altered habitats, such as landfills, are hotspots for the acquisition and spread of high-risk ESC E. coli lineages associated with hospital infections. Measures must be implemented to limit their spread into natural environments.
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Affiliation(s)
- Judith Guitart-Matas
- Joint Research Unit IRTA-UAB in Animal Health, Animal Health Research Centre (CReSA), Autonomous University of Barcelona (UAB), Catalonia, Spain; Institute of Agrifood Research and Technology (IRTA), Animal Health Program (CReSA), WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe, Autonomous University of Barcelona (UAB), Catalonia, Spain
| | - Johan Espunyes
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Catalonia, Spain
| | - Lucia Illera
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Catalonia, Spain
| | | | - Maria Puig Ribas
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Catalonia, Spain
| | - Ignasi Marco
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Catalonia, Spain
| | - Lourdes Migura-Garcia
- Joint Research Unit IRTA-UAB in Animal Health, Animal Health Research Centre (CReSA), Autonomous University of Barcelona (UAB), Catalonia, Spain; Institute of Agrifood Research and Technology (IRTA), Animal Health Program (CReSA), WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe, Autonomous University of Barcelona (UAB), Catalonia, Spain.
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Petrocchi Rilo M, Gutiérrez Martín CB, Acebes Fernández V, Aguarón Turrientes Á, González Fernández A, Miguélez Pérez R, Martínez Martínez S. Streptococcus suis Research Update: Serotype Prevalence and Antimicrobial Resistance Distribution in Swine Isolates Recovered in Spain from 2020 to 2022. Vet Sci 2024; 11:40. [PMID: 38250946 PMCID: PMC10819597 DOI: 10.3390/vetsci11010040] [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: 11/28/2023] [Revised: 12/29/2023] [Accepted: 01/13/2024] [Indexed: 01/23/2024] Open
Abstract
This study aimed to update the Streptococcus suis serotype distribution in Spain by analysing 302 clinical isolates recovered from diseased pigs between 2020 and 2022. The main objectives were to identify prevalent serotypes, differentiate specific serotypes 1, 14, 2, and 1/2, investigate specific genotypic and phenotypic antimicrobial resistance features, and explore associations between resistance genes and phenotypic resistances. Serotypes 9 (21.2%), 1 (16.2%), 2 (15.6%), 3 (6%), and 7 (5.6%) were the most prevalent, whereas serotypes 14 and 1/2 corresponded with 4.3% and 0.7% of all isolates. Antimicrobial resistance genes, including tet(O), erm(B), lnu(B), lsa(E), tet(M), and mef(A/E), were analysed, which were present in 85.8%, 65.2%, 7%, 7%, 6.3%, and 1% of the samples, respectively. Susceptibility testing for 18 antimicrobials revealed high resistance levels, particularly for clindamycin (88.4%), chlortetracycline (89.4%), and sulfadimethoxine (94.4%). Notably, seven significant associations (p < 0.0001) were detected, correlating specific antimicrobial resistance genes to the observed phenotypic resistance. These findings contribute to understanding the S. suis serotype distribution and its antibiotic resistance profiles in Spain, offering valuable insights for veterinary and public health efforts in managing S. suis-associated infections.
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Affiliation(s)
- Máximo Petrocchi Rilo
- Animal Health Department, Veterinary Medicine Faculty, University of León, Campus de Vegazana s/n, 24071 León, Spain; (M.P.R.); (C.B.G.M.); (V.A.F.); (A.G.F.); (R.M.P.)
| | - César Bernardo Gutiérrez Martín
- Animal Health Department, Veterinary Medicine Faculty, University of León, Campus de Vegazana s/n, 24071 León, Spain; (M.P.R.); (C.B.G.M.); (V.A.F.); (A.G.F.); (R.M.P.)
| | - Vanessa Acebes Fernández
- Animal Health Department, Veterinary Medicine Faculty, University of León, Campus de Vegazana s/n, 24071 León, Spain; (M.P.R.); (C.B.G.M.); (V.A.F.); (A.G.F.); (R.M.P.)
| | | | - Alba González Fernández
- Animal Health Department, Veterinary Medicine Faculty, University of León, Campus de Vegazana s/n, 24071 León, Spain; (M.P.R.); (C.B.G.M.); (V.A.F.); (A.G.F.); (R.M.P.)
| | - Rubén Miguélez Pérez
- Animal Health Department, Veterinary Medicine Faculty, University of León, Campus de Vegazana s/n, 24071 León, Spain; (M.P.R.); (C.B.G.M.); (V.A.F.); (A.G.F.); (R.M.P.)
| | - Sonia Martínez Martínez
- Animal Health Department, Veterinary Medicine Faculty, University of León, Campus de Vegazana s/n, 24071 León, Spain; (M.P.R.); (C.B.G.M.); (V.A.F.); (A.G.F.); (R.M.P.)
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217
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Kuhnert P, Brodard I, Ackermann S, Schierack P, Jores J. Serological and molecular detection as well as typing of Leptospira spp. in foxes, raccoons, and other wild carnivores in North-Eastern Germany, 2021-2022. Heliyon 2024; 10:e23268. [PMID: 38163163 PMCID: PMC10756992 DOI: 10.1016/j.heliyon.2023.e23268] [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: 06/06/2023] [Revised: 10/20/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
Leptospirosis is a worldwide zoonosis caused by pathogenic Leptospira spp. While the latter are reported from various mammal hosts such as humans, dogs, or rodents, less is known about their presence in wild carnivores. We therefore investigated the presence of Leptospira spp. in foxes, raccoons, badgers, raccoon dogs, and martens in North-Eastern Germany. Kidney, urine, and blood specimens obtained from legally hunted or road-killed animals were tested by real-time PCR and by serogroup specific antibody detection for the presence of Leptospira spp. Additionally, kidney and urine specimens were tested by real-time PCR for the presence of Brucella spp. and Francisella tularensis, with all being negative for these two zoonotic pathogens. Leptospira spp. were detected by PCR in 12.6 % (n = 21/166) and serologically in 26.2 % (n = 53/202) of tissue and serum samples, respectively. Antibodies to 15 different serogroups were identified with Javanica (n = 25) and Bataviae (n = 12) being predominant. A high sero-prevalence of 34.0 % and 18.6 % in foxes and raccoons, respectively, and the presence of ST17 associated with human and animal leptospirosis indicates a reservoir and the zoonotic potential of these wild animals.
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Affiliation(s)
- Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Isabelle Brodard
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Stefanie Ackermann
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Peter Schierack
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology, Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences Brandenburg, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Joerg Jores
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
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218
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Manna S, Werren JP, Ortika BD, Bellich B, Pell CL, Nikolaou E, Gjuroski I, Lo S, Hinds J, Tundev O, Dunne EM, Gessner BD, Bentley SD, Russell FM, Mulholland EK, Mungun T, von Mollendorf C, Licciardi PV, Cescutti P, Ravenscroft N, Hilty M, Satzke C. Streptococcus pneumoniae serotype 33G: genetic, serological, and structural analysis of a new capsule type. Microbiol Spectr 2024; 12:e0357923. [PMID: 38059623 PMCID: PMC10782959 DOI: 10.1128/spectrum.03579-23] [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: 10/04/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE Streptococcus pneumoniae (the pneumococcus) is a bacterial pathogen with the greatest burden of disease in Asia and Africa. The pneumococcal capsular polysaccharide has biological relevance as a major virulence factor as well as public health importance as it is the target for currently licensed vaccines. These vaccines have limited valency, covering up to 23 of the >100 known capsular types (serotypes) with higher valency vaccines in development. Here, we have characterized a new pneumococcal serotype, which we have named 33G. We detected serotype 33G in nasopharyngeal swabs (n = 20) from children and adults hospitalized with pneumonia, as well as healthy children in Mongolia. We show that the genetic, serological, and biochemical properties of 33G differ from existing serotypes, satisfying the criteria to be designated as a new serotype. Future studies should focus on the geographical distribution of 33G and any changes in prevalence following vaccine introduction.
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Affiliation(s)
- Sam Manna
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Pediatrics, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Joel P. Werren
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Belinda D. Ortika
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Barbara Bellich
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Casey L. Pell
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Elissavet Nikolaou
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ilche Gjuroski
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Stephanie Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Jason Hinds
- Institute for Infection and Immunity, St. George’s, University of London, London, United Kingdom
- BUGS Bioscience, London Bioscience Innovation Center, London, United Kingdom
| | - Odgerel Tundev
- National Center for Communicable Diseases, Ministry of Health, Ulaanbaatar, Mongolia
| | | | | | - Stephen D. Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Fiona M. Russell
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Pediatrics, The University of Melbourne, Melbourne, Australia
| | - E. Kim Mulholland
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Tuya Mungun
- National Center for Communicable Diseases, Ministry of Health, Ulaanbaatar, Mongolia
| | - Claire von Mollendorf
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Pediatrics, The University of Melbourne, Melbourne, Australia
| | - Paul V. Licciardi
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Pediatrics, The University of Melbourne, Melbourne, Australia
| | - Paola Cescutti
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch, South Africa
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Catherine Satzke
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Pediatrics, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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219
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Sakaguchi YM, Murakami K, Akebo H, Sada RM, Abe N, Maeda T, Goto M, Takahashi T, Takahashi Y, Kashihara E, Shim J, Miyake H, Hatta K. Successful treatment of streptococcal toxic shock syndrome complicated by primary peritonitis and bilateral empyema in a healthy young woman: Identification of uncommon clone emm103 and novel sequence type 1363. IDCases 2024; 35:e01927. [PMID: 38303733 PMCID: PMC10831287 DOI: 10.1016/j.idcr.2024.e01927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/13/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024] Open
Abstract
Streptococcal toxic shock syndrome (STSS) has a dramatic clinical course and high mortality rate. Here, we report a case of STSS complicated by primary peritonitis and bilateral empyema. A previously healthy young woman was diagnosed with STSS complicated by primary peritonitis and bilateral empyema. Blood culture results on admission were negative. Sever shock, respiratory failure, systemic inflammation, thrombocytopenia, renal failure, ascites, and pleural effusion occurred, mimicking thrombocytopenia, anasarca, fever, reticulin fibrosis/renal failure and organomegaly (TAFRO) syndrome. Retesting blood cultures identified Streptococcus pyogenes. Gram staining of ascites and pleural fluid indicated gram-positive cocci in chains. Antibiotics, immunoglobulins, and surgical intervention led to recovery without complications. Ex-post genotypic analyses showed uncommon emm103.0 (cluster E3) of emm long sequence (784 base) and novel sequence type 1363. STSS diagnosis can be difficult as it mimics other systemic inflammatory diseases. Therefore, it is crucial for clinicians to perform microbiological examinations from infection foci, even if the initial culture is negative.
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Affiliation(s)
- Yoshihiko M. Sakaguchi
- Department of General Internal Medicine, Tenri Hospital, Nara, Japan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
- Ph.D. Program in Humanics, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Koichiro Murakami
- Department of General Internal Medicine, Tenri Hospital, Nara, Japan
| | - Hiroyuki Akebo
- Department of General Internal Medicine, Tenri Hospital, Nara, Japan
| | - Ryuichi Minoda Sada
- Department of General Internal Medicine, Tenri Hospital, Nara, Japan
- Department of Transformative Protection to Infectious Disease, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Infection Control, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Noriyuki Abe
- Department of Clinical Laboratory Medicine, Tenri Hospital, Nara, Japan
| | - Takahiro Maeda
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Mieko Goto
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Takashi Takahashi
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Yusuke Takahashi
- Department of General Internal Medicine, Tenri Hospital, Nara, Japan
- Department of Infection Control, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Eriko Kashihara
- Department of General Internal Medicine, Tenri Hospital, Nara, Japan
| | - Jaegi Shim
- Department of General Internal Medicine, Tenri Hospital, Nara, Japan
| | - Hirofumi Miyake
- Department of General Internal Medicine, Tenri Hospital, Nara, Japan
| | - Kazuhiro Hatta
- Department of General Internal Medicine, Tenri Hospital, Nara, Japan
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220
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Garcia-Fernandez A, Janowicz A, Marotta F, Napoleoni M, Arena S, Primavilla S, Pitti M, Romantini R, Tomei F, Garofolo G, Villa L. Antibiotic resistance, plasmids, and virulence-associated markers in human strains of Campylobacter jejuni and Campylobacter coli isolated in Italy. Front Microbiol 2024; 14:1293666. [PMID: 38260875 PMCID: PMC10800408 DOI: 10.3389/fmicb.2023.1293666] [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: 09/13/2023] [Accepted: 12/07/2023] [Indexed: 01/24/2024] Open
Abstract
Campylobacteriosis, a prevalent foodborne gastrointestinal infection in Europe, is primarily caused by Campylobacter jejuni and Campylobacter coli, with rising global concerns over antimicrobial resistance in these species. This study comprehensively investigates 133 human-origin Campylobacter spp. strains (102 C. jejuni and 31 C. coli) collected in Italy from 2013 to 2021. The predominant Multilocus Sequence Typing Clonal complexes (CCs) were ST-21 CC and ST-206 CC in C. jejuni and ST-828 CC in C. coli. Ciprofloxacin and tetracycline resistance, mainly attributed to GyrA (T86I) mutation and tet(O) presence, were prevalent, while erythromycin resistance was associated with 23S rRNA gene mutation (A2075G), particularly in C. coli exhibiting multidrug-resistant pattern CipTE. Notable disparities in virulence factors among strains were observed, with C. jejuni exhibiting a higher abundance compared to C. coli. Notably, specific C. jejuni sequence types, including ST-21, ST-5018, and ST-1263, demonstrated significantly elevated counts of virulence genes. This finding underscores the significance of considering both the species and strain-level variations in virulence factor profiles, shedding light on potential differences in the pathogenicity and clinical outcomes associated with distinct C. jejuni lineages. Campylobacter spp. plasmids were classified into three groups comprising pVir-like and pTet-like plasmids families, exhibiting diversity among Campylobacter spp. The study underscores the importance of early detection through Whole Genome Sequencing to identify potential emergent virulence, resistance/virulence plasmids, and new antimicrobial resistance markers. This approach provides actionable public health data, supporting the development of robust surveillance programs in Italy.
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Affiliation(s)
| | - Anna Janowicz
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Francesca Marotta
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Maira Napoleoni
- Centro di Riferimento Regionale Patogeni Enterici, CRRPE, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “T. Rosati”, Perugia, Italy
| | - Sergio Arena
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Sara Primavilla
- Centro di Riferimento Regionale Patogeni Enterici, CRRPE, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “T. Rosati”, Perugia, Italy
| | - Monica Pitti
- Centro di Riferimento per la Tipizzazione delle Salmonelle, CeRTiS, Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Turin, Italy
| | - Romina Romantini
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | | | - Giuliano Garofolo
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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221
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Tönnies H, Heep A, Herrmann J, Lange M, Mellmann A, Hamprecht A. Investigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing. Antimicrob Resist Infect Control 2024; 13:1. [PMID: 38184647 PMCID: PMC10771705 DOI: 10.1186/s13756-023-01359-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND We analyzed an outbreak of Bacillus cereus group (Bcg) at a single-center neonatal intensive care unit level IV by conducting comprehensive sampling of both patients and the environment. METHODS Between 06/2020 and 10/2021, all Bcg isolates identified by both regular colonization screening and additional sampling of the environment were subjected to whole-genome sequencing, followed by in vitro extraction of MLST ST, resistance genes and virulence factors. Using publicly available genome sequences, we defined an ad hoc core genome multilocus sequence typing (cgMLST) scheme comprising 2759 target genes for Bcg typing, which we applied to the detected isolates. We have compared the results with a stable cgMLST that was published in the meantime and completed the investigation with a SNP analysis. RESULTS We analyzed 28 Bcg isolates from patient and environmental samples using MLST and cgMLST. This revealed multiple sequence types, with ST127 being the most common (n = 13). Both cgMLST schemes grouped ten of the 13 ST127 isolates into a cluster, including two invasive isolates from two different patients and several environmental samples. SNP analysis postulated a screen from a ventilation machine as a possible reservoir. CONCLUSION In sensitive settings such as neonatal intensive care units, considering the environment in outbreak analyses is crucial, especially when investigating potential transmission routes through shared devices. When dealing with widespread bacteria such as Bcg, high-resolution typing techniques are necessary. In this study, we successfully resolved an outbreak of Bcg infections using a custom cgMLST scheme combined with a SNP analysis.
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Affiliation(s)
- Hauke Tönnies
- Institute of Hygiene, University Hospital Münster, Münster, Germany.
| | - Axel Heep
- Department of Pediatrics, Elisabeth Children's Hospital, University of Oldenburg, Oldenburg, Germany
| | - Jörg Herrmann
- Institute of Hygiene, University Hospital Oldenburg, Oldenburg, Germany
| | - Matthias Lange
- Department of Pediatrics, Elisabeth Children's Hospital, University of Oldenburg, Oldenburg, Germany
| | | | - Axel Hamprecht
- Institute of Medical Microbiology and Virology, University Hospital Oldenburg, Oldenburg, Germany
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222
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Guo C, Chen Q, Fan G, Sun Y, Nie J, Shen Z, Meng Z, Zhou Y, Li S, Wang S, Ma J, Sun Q, Wu L. gcPathogen: a comprehensive genomic resource of human pathogens for public health. Nucleic Acids Res 2024; 52:D714-D723. [PMID: 37850635 PMCID: PMC10767814 DOI: 10.1093/nar/gkad875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
Here, we present the manually curated Global Catalogue of Pathogens (gcPathogen), an extensive genomic resource designed to facilitate rapid and accurate pathogen analysis, epidemiological exploration and monitoring of antibiotic resistance features and virulence factors. The catalogue seamlessly integrates and analyzes genomic data and associated metadata for human pathogens isolated from infected patients, animal hosts, food and the environment. The pathogen list is supported by evidence from medical or government pathogenic lists and publications. The current version of gcPathogen boasts an impressive collection of 1 164 974 assemblies comprising 986 044 strains from 497 bacterial taxa, 4794 assemblies encompassing 4319 strains from 265 fungal taxa, 89 965 assemblies featuring 13 687 strains from 222 viral taxa, and 646 assemblies including 387 strains from 159 parasitic taxa. Through this database, researchers gain access to a comprehensive 'one-stop shop' that facilitates global, long-term public health surveillance while enabling in-depth analysis of genomes, sequence types, antibiotic resistance genes, virulence factors and mobile genetic elements across different countries, diseases and hosts. To access and explore the data and statistics, an interactive web interface has been developed, which can be accessed at https://nmdc.cn/gcpathogen/. This user-friendly platform allows seamless querying and exploration of the extensive information housed within the gcPathogen database.
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Affiliation(s)
- Chongye Guo
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Qi Chen
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Guomei Fan
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Yan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Jingyi Nie
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Zhihong Shen
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhen Meng
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Yuanchun Zhou
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Shiwen Li
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Shuai Wang
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Juncai Ma
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinglan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Linhuan Wu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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223
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Baker M, Zhang X, Maciel-Guerra A, Babaarslan K, Dong Y, Wang W, Hu Y, Renney D, Liu L, Li H, Hossain M, Heeb S, Tong Z, Pearcy N, Zhang M, Geng Y, Zhao L, Hao Z, Senin N, Chen J, Peng Z, Li F, Dottorini T. Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China. Nat Commun 2024; 15:206. [PMID: 38182559 PMCID: PMC10770378 DOI: 10.1038/s41467-023-44272-1] [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: 04/04/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024] Open
Abstract
Sharing of genetic elements among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 Escherichia coli and Salmonella enterica isolates collected within and across hosts and environments, in 10 Chinese chicken farms over 2.5 years using data-mining methods. Most isolates within same hosts possessed the same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Supervised machine learning classifiers revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials, primarily associated with resistance in E. coli and susceptibility in S. enterica. Many were essential and affected same metabolic processes in both species, albeit with varying degrees of phylogenetic penetration. Multi-modal strategies are crucial to investigate the interplay of mobilome, resistance and metabolism in cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.
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Affiliation(s)
- Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Xibin Zhang
- Shandong New Hope Liuhe Group Co. Ltd. and Qingdao Key Laboratory of Animal Feed Safety, Qingdao, Shandong, 266000, P.R. China
| | - Alexandre Maciel-Guerra
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Kubra Babaarslan
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - David Renney
- Nimrod Veterinary Products Limited, 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh, GL56 0JQ, London, UK
| | - Longhai Liu
- Shandong Kaijia Food Co. Ltd, Weifang, P. R. China
| | - Hui Li
- Luoyang Center for Disease Control and Prevention, No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province, Luolong, 471000, P. R. China
| | - Maqsud Hossain
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Stephan Heeb
- School of Life Sciences, University of Nottingham, East Drive, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - Zhiqin Tong
- Luoyang Center for Disease Control and Prevention, No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province, Luolong, 471000, P. R. China
| | - Nicole Pearcy
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
- School of Life Sciences, University of Nottingham, East Drive, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - Meimei Zhang
- Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District, Shenyang City, Liaoning Province, 110072, P. R. China
| | - Yingzhi Geng
- Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District, Shenyang City, Liaoning Province, 110072, P. R. China
| | - Li Zhao
- Agricultural Biopharmaceutical Laboratory, College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao City, Shandong Province, 266109, P. R. China
| | - Zhihui Hao
- Chinese Veterinary Medicine Innovation Center, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing City, 100193, P. R. China
| | - Nicola Senin
- Department of Engineering, University of Perugia, Perugia, I06125, Italy
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK.
- Centre for Smart Food Research, Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, 315100, P. R. China.
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Monecke S, Braun SD, Collatz M, Diezel C, Müller E, Reinicke M, Cabal Rosel A, Feßler AT, Hanke D, Loncaric I, Schwarz S, Cortez de Jäckel S, Ruppitsch W, Gavier-Widén D, Hotzel H, Ehricht R. Molecular Characterization of Chimeric Staphylococcus aureus Strains from Waterfowl. Microorganisms 2024; 12:96. [PMID: 38257923 PMCID: PMC10821479 DOI: 10.3390/microorganisms12010096] [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: 11/10/2023] [Revised: 12/15/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
Staphylococcus aureus is a versatile pathogen that does not only occur in humans but also in various wild and domestic animals, including several avian species. When characterizing S. aureus isolates from waterfowl, isolates were identified as atypical CC133 by DNA microarray analysis. They differed from previously sequenced CC133 strains in the presence of the collagen adhesin gene cna; some also showed a different capsule type and a deviant spa type. Thus, they were subjected to whole-genome sequencing. This revealed multiple insertions of large regions of DNA from other S. aureus lineages into a CC133-derived backbone genome. Three distinct strains were identified based on the size and extent of these inserts. One strain comprised two small inserts of foreign DNA up- and downstream of oriC; one of about 7000 nt or 0.25% originated from CC692 and the other, at ca. 38,000 nt or 1.3% slightly larger one was of CC522 provenance. The second strain carried a larger CC692 insert (nearly 257,000 nt or 10% of the strain's genome), and its CC522-derived insert was also larger, at about 53,500 nt or 2% of the genome). The third strain carried an identical CC692-derived region (in which the same mutations were observed as in the second strain), but it had a considerably larger CC522-like insertion of about 167,000 nt or 5.9% of the genome. Both isolates of the first, and two out of four isolates of the second strain also harbored a hemolysin-beta-integrating prophage carrying "bird-specific" virulence factors, ornithine cyclodeaminase D0K6J8 and a putative protease D0K6J9. Furthermore, isolates had two different variants of SCC elements that lacked mecA/mecC genes. These findings highlight the role of horizontal gene transfer in the evolution of S. aureus facilitated by SCC elements, by phages, and by a yet undescribed mechanism for large-scale exchange of core genomic DNA.
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Affiliation(s)
- Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute for Medical Microbiology and Virology, Dresden University Hospital, 01307 Dresden, Germany
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Maximillian Collatz
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Celia Diezel
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Elke Müller
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Martin Reinicke
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Adriana Cabal Rosel
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, 1220 Vienna, Austria
| | - Andrea T. Feßler
- Institute of Microbiology and Epizootics, Centre for Infection, Medicine School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Dennis Hanke
- Institute of Microbiology and Epizootics, Centre for Infection, Medicine School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection, Medicine School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, 1220 Vienna, Austria
| | - Dolores Gavier-Widén
- Department of Pathology and Wildlife Disease, National Veterinary Institute (SVA), 75189 Uppsala, Sweden
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), 75007 Uppsala, Sweden
| | - Helmut Hotzel
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), 07743 Jena, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich-Schiller University, 07743 Jena, Germany
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225
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Jiang N, Chen H, Cheng L, Fu Q, Liu R, Liang Q, Fu G, Wan C, Huang Y. Genomic analysis reveals the population structure and antimicrobial resistance of avian Pasteurella multocida in China. J Antimicrob Chemother 2024; 79:186-194. [PMID: 38019670 DOI: 10.1093/jac/dkad365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
OBJECTIVES To investigate the population structure and antimicrobial resistance (AMR) of avian Pasteurella multocida in China. METHODS Utilizing WGS analysis, we explored the phylogeny using a dataset of 546 genomes, comprising avian P. multocida isolates from China (n = 121), the USA (n = 165), Australia(n = 153), Bangladesh (n = 3) and isolates of other hosts from China (n = 104). We examined the integrative and conjugative element (ICE) structures and the distribution of their components carrying resistance genes, and reconstructed the evolutionary history of A:L1:ST129 (n = 110). RESULTS The population structure of avian P. multocida in China was dominated by the A:L1:ST129 clone with limited genetic diversity. A:L1:ST129 isolates possessed a broader spectrum of resistance genes at comparatively higher frequencies than those from other hosts and countries. The novel putative ICEs harboured complex resistant clusters that were prevalent in A:L1:ST129. Bayesian analysis predicted that the A:L1:ST129 clone emerged around 1923, and evolved slowly. CONCLUSIONS A:L1:ST129 appears to possess a host predilection towards avian species in China, posing a potential health threat to other animals. The complex AMR determinants coupled with high frequencies may strengthen the population dominance of A:L1:ST129. The extensive antimicrobial utilization in poultry farming and the mixed rearing practices could have accelerated AMR accumulation in A:L1:ST129. ICEs, together with their resistant clusters, significantly contribute to resistance gene transfer and facilitate the adaptation of A:L1:ST129 to ecological niches. Despite the genetic stability and slow evolution rate, A:L1:ST129 deserves continued monitoring due to its propensity to retain resistance genes, warranting global attention to preclude substantial economic losses.
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Affiliation(s)
- Nansong Jiang
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Hongmei Chen
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Longfei Cheng
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Qiuling Fu
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Rongchang Liu
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Qizhang Liang
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Guanghua Fu
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Chunhe Wan
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Yu Huang
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
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226
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Huong LQ, Chisnall T, Rodgers JD, Cawthraw SA, Card RM. Prevalence, antibiotic resistance, and genomic characterisation of Campylobacter spp. in retail chicken in Hanoi, Vietnam. Microb Genom 2024; 10:001190. [PMID: 38294872 PMCID: PMC10868608 DOI: 10.1099/mgen.0.001190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/20/2024] [Indexed: 02/01/2024] Open
Abstract
Campylobacter spp. are a leading cause of bacterial foodborne zoonosis worldwide, with poultry meat and products recognised as a significant source of human infection. In Vietnam there are few data regarding the occurrence, antimicrobial resistance, and genomic diversity of Campylobacter in poultry and poultry meat. The aim of this study was to estimate the prevalence of Campylobacter in chicken meat at retail in Hanoi, determine antimicrobial sensitivities of the Campylobacter isolated, and assess their genetic diversity. A total of 120 chicken meat samples were collected from eight traditional retail markets (n=80) and four supermarkets (n=40). Campylobacter was isolated following ISO 10272-1 : 2017 and identification verified by PCR. The prevalence of Campylobacter was 38.3 % (46/120) and C. coli was the most prevalent species in both retail markets (74 %) and supermarkets (88 %). The minimum inhibitory concentrations for ciprofloxacin, erythromycin, gentamicin, nalidixic acid, streptomycin, and tetracycline were determined by broth microdilution for 32 isolates. All characterised Campylobacter were resistant to ciprofloxacin, nalidixic acid, and tetracycline, with corresponding resistance determinants detected in the sequenced genomes. Most C. coli were multidrug resistant (24/28) and two harboured the erythromycin resistance gene ermB on a multiple drug-resistance genomic island, a potential mechanism for dissemination of resistance. The 32 isolates belonged to clonal complexes associated with both poultry and people, such as CC828 for C. coli. These results contribute to the One Health approach for addressing Campylobacter in Vietnam by providing detailed new insights into a main source of human infection and can inform the design of future surveillance approaches.
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Affiliation(s)
- Luu Quynh Huong
- National Institute of Veterinary Research (NIVR), 86 Truong Chinh Road, Dong Da district, Hanoi, Vietnam
| | - Thomas Chisnall
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, UK
| | - John D. Rodgers
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, UK
| | - Shaun A. Cawthraw
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, UK
| | - Roderick M. Card
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, UK
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227
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Trouche B, Schrieke H, Duron O, Eren AM, Reveillaud J. Wolbachia populations across organs of individual Culex pipiens: highly conserved intra-individual core pangenome with inter-individual polymorphisms. ISME COMMUNICATIONS 2024; 4:ycae078. [PMID: 38915450 PMCID: PMC11195471 DOI: 10.1093/ismeco/ycae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 04/26/2024] [Accepted: 06/06/2024] [Indexed: 06/26/2024]
Abstract
Wolbachia is a maternally inherited intracellular bacterium that infects a wide range of arthropods including mosquitoes. The endosymbiont is widely used in biocontrol strategies due to its capacity to modulate arthropod reproduction and limit pathogen transmission. Wolbachia infections in Culex spp. are generally assumed to be monoclonal but the potential presence of genetically distinct Wolbachia subpopulations within and between individual organs has not been investigated using whole genome sequencing. Here we reconstructed Wolbachia genomes from ovary and midgut metagenomes of single naturally infected Culex pipiens mosquitoes from Southern France to investigate patterns of intra- and inter-individual differences across mosquito organs. Our analyses revealed a remarkable degree of intra-individual conservancy among Wolbachia genomes from distinct organs of the same mosquito both at the level of gene presence-absence signal and single-nucleotide polymorphisms (SNPs). Yet, we identified several synonymous and non-synonymous substitutions between individuals, demonstrating the presence of some level of genomic heterogeneity among Wolbachia that infect the same C. pipiens field population. Overall, the absence of genetic heterogeneity within Wolbachia populations in a single individual confirms the presence of a dominant Wolbachia that is maintained under strong purifying forces of evolution.
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Affiliation(s)
- Blandine Trouche
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
| | - Hans Schrieke
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
| | - Olivier Duron
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
| | - A Murat Eren
- Marine Biological Laboratory, Woods Hole, MA 02543, United States
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, 26129 Oldenburg, Germany
| | - Julie Reveillaud
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
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228
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Chattaway MA. Analysis of Whole Genome Sequencing Data for Detection of Antimicrobial Resistance Determinants. Methods Mol Biol 2024; 2833:211-223. [PMID: 38949713 DOI: 10.1007/978-1-0716-3981-8_19] [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: 07/02/2024]
Abstract
Genomic sequencing has revolutionized microbial typing methods and transformed high-throughput methods in reference, clinical, and research laboratories. The detection of antimicrobial-resistant (AMR) determinants using genomic methods can provide valuable information on the emergence of resistance. Here we describe an approach to detecting AMR determinants using an open access and freely available platform which does not require bioinformatic expertise.
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Affiliation(s)
- Marie Anne Chattaway
- Gastrointestinal Bacteria Unit, United Kingdom Health Security Agency, London, UK.
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229
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Carhuaricra-Huaman D, Setubal JC. Step-by-Step Bacterial Genome Comparison. Methods Mol Biol 2024; 2802:107-134. [PMID: 38819558 DOI: 10.1007/978-1-0716-3838-5_5] [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: 06/01/2024]
Abstract
Thanks to advancements in genome sequencing and bioinformatics, thousands of bacterial genome sequences are available in public databases. This presents an opportunity to study bacterial diversity in unprecedented detail. This chapter describes a complete bioinformatics workflow for comparative genomics of bacterial genomes, including genome annotation, pangenome reconstruction and visualization, phylogenetic analysis, and identification of sequences of interest such as antimicrobial-resistance genes, virulence factors, and phage sequences. The workflow uses state-of-the-art, open-source tools. The workflow is presented by means of a comparative analysis of Salmonella enterica serovar Typhimurium genomes. The workflow is based on Linux commands and scripts, and result visualization relies on the R environment. The chapter provides a step-by-step protocol that researchers with basic expertise in bioinformatics can easily follow to conduct investigations on their own genome datasets.
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Affiliation(s)
- Dennis Carhuaricra-Huaman
- Programa de Pós-Graduação Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, Sao Paulo, SP, Brazil
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, San Borja, Lima, Peru
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil.
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230
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Cappelli L, Cinelli P, Perrotta A, Veggi D, Audagnotto M, Tuscano G, Pansegrau W, Bartolini E, Rinaudo D, Cozzi R. Computational structure-based approach to study chimeric antigens using a new protein scaffold displaying foreign epitopes. FASEB J 2024; 38:e23326. [PMID: 38019196 DOI: 10.1096/fj.202202130r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 10/24/2023] [Accepted: 11/08/2023] [Indexed: 11/30/2023]
Abstract
The identification and recombinant production of functional antigens and/or epitopes of pathogens represent a crucial step for the development of an effective protein-based vaccine. Many vaccine targets are outer membrane proteins anchored into the lipidic bilayer through an extended hydrophobic portion making their recombinant production challenging. Moreover, only the extracellular loops, and not the hydrophobic regions, are naturally exposed to the immune system. In this work, the Domain 3 (D3) from Group B Streptococcus (GBS) pilus 2a backbone protein has been identified and engineered to be used as a scaffold for the display of extracellular loops of two Neisseria gonorrhoeae membrane proteins (PorB.1b and OpaB). A computational structure-based approach has been applied to the design of both the scaffold and the model antigens. Once identified the best D3 engineerable site, several different chimeric D3 displaying PorB.1b and OpaB extracellular loops were produced as soluble proteins. Each molecule has been characterized in terms of solubility, stability, and ability to correctly display the foreign epitope. This antigen dissection strategy allowed the identification of most immunogenic extracellular loops of both PorB.1b and OpaB gonococcal antigens. The crystal structure of chimeric D3 displaying PorB.1b immunodominant loop has been obtained confirming that the engineerization did not alter the predicted native structure of this epitope. Taken together, the reported data suggest that D3 is a novel protein scaffold for epitope insertion and display, and a valid alternative to the production of whole membrane protein antigens. Finally, this work describes a generalized computational structure-based approach for the identification, design, and dissection of epitopes in target antigens through chimeric proteins.
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Affiliation(s)
- Luigia Cappelli
- Dipartimento di Farmacia e Biotecnologie - FaBiT, University of Bologna, Bologna, Italy
- GSK, Siena, Italy
| | - Paolo Cinelli
- Dipartimento di Farmacia e Biotecnologie - FaBiT, University of Bologna, Bologna, Italy
- GSK, Siena, Italy
| | - Andrea Perrotta
- GSK, Siena, Italy
- Dipartimento di Scienze della Vita, University of Siena, Siena, Italy
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231
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Cribb DM, Moffatt CRM, Wallace RL, McLure AT, Bulach D, Jennison AV, French N, Valcanis M, Glass K, Kirk MD. Genomic and clinical characteristics of campylobacteriosis in Australia. Microb Genom 2024; 10:001174. [PMID: 38214338 PMCID: PMC10868609 DOI: 10.1099/mgen.0.001174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024] Open
Abstract
Campylobacter spp. are a common cause of bacterial gastroenteritis in Australia, primarily acquired from contaminated meat. We investigated the relationship between genomic virulence characteristics and the severity of campylobacteriosis, hospitalisation, and other host factors.We recruited 571 campylobacteriosis cases from three Australian states and territories (2018-2019). We collected demographic, health status, risk factors, and self-reported disease data. We whole genome sequenced 422 C. jejuni and 84 C. coli case isolates along with 616 retail meat isolates. We classified case illness severity using a modified Vesikari scoring system, performed phylogenomic analysis, and explored risk factors for hospitalisation and illness severity.On average, cases experienced a 7.5 day diarrhoeal illness with additional symptoms including stomach cramps (87.1 %), fever (75.6 %), and nausea (72.0 %). Cases aged ≥75 years had milder symptoms, lower Vesikari scores, and higher odds of hospitalisation compared to younger cases. Chronic gastrointestinal illnesses also increased odds of hospitalisation. We observed significant diversity among isolates, with 65 C. jejuni and 21 C. coli sequence types. Antimicrobial resistance genes were detected in 20.4 % of isolates, but multidrug resistance was rare (0.04 %). Key virulence genes such as cdtABC (C. jejuni) and cadF were prevalent (>90 % presence) but did not correlate with disease severity or hospitalisation. However, certain genes (e.g. fliK, Cj1136, and Cj1138) appeared to distinguish human C. jejuni cases from food source isolates.Campylobacteriosis generally presents similarly across cases, though some are more severe. Genotypic virulence factors identified in the literature to-date do not predict disease severity but may differentiate human C. jejuni cases from food source isolates. Host factors like age and comorbidities have a greater influence on health outcomes than virulence factors.
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Affiliation(s)
- Danielle M. Cribb
- National Centre for Epidemiology and Population Health, the Australian National University, Canberra, Australia
| | - Cameron R. M. Moffatt
- Queensland Health Forensic and Scientific Services, Coopers Plains, Brisbane, Australia
| | - Rhiannon L. Wallace
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, British Columbia, Canada
| | - Angus T. McLure
- National Centre for Epidemiology and Population Health, the Australian National University, Canberra, Australia
| | - Dieter Bulach
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Amy V. Jennison
- Queensland Health Forensic and Scientific Services, Coopers Plains, Brisbane, Australia
| | - Nigel French
- Tāwharau Ora|School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Kathryn Glass
- National Centre for Epidemiology and Population Health, the Australian National University, Canberra, Australia
| | - Martyn D. Kirk
- National Centre for Epidemiology and Population Health, the Australian National University, Canberra, Australia
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232
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Esposito A, Piazza S. Broad Genome Sequencing of Environmental and Clinical Strains and Genotyping. Methods Mol Biol 2024; 2721:171-181. [PMID: 37819522 DOI: 10.1007/978-1-0716-3473-8_12] [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: 10/13/2023]
Abstract
The Next-Generation Sequencing revolution had a great impact on the genomics of Pseudomonas aeruginosa. Since the first release of the P. aeruginosa PAO1 genome, there are more than 5700 genomes published. This wealth of information has been accompanied by the development of bioinformatic tools for handling genomic and phenotypic data. Bioinformatics, indeed, become de facto a big data science. In this chapter, we give a brief historical overview of the knowledge gained from P. aeruginosa genome sequencing, then we describe the wet-lab procedure to extract the DNA and prepare the library for broad genome sequencing using Illumina MiSeq technology. As last, we describe three user-friendly bioinformatics procedures to infer the P. aeruginosa genotype, starting from NGS data, with the Multi-Locus Sequence Typing method, and visualize it as a minimum spanning tree.
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Affiliation(s)
- Alfonso Esposito
- Faculty of Medicine and Surgery, "Kore" University of Enna, Enna, Italy.
| | - Silvano Piazza
- Computational Biology Unit, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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Hakimi M, Ye F, Stinman CC, Sahin O, Burrough ER. Antimicrobial susceptibility of U.S. porcine Brachyspira isolates and genetic diversity of B. hyodysenteriae by multilocus sequence typing. J Vet Diagn Invest 2024; 36:62-69. [PMID: 37968893 PMCID: PMC10734594 DOI: 10.1177/10406387231212189] [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: 11/17/2023] Open
Abstract
Swine dysentery, caused by Brachyspira hyodysenteriae and the newly recognized Brachyspira hampsonii in grower-finisher pigs, is a substantial economic burden in many swine-rearing countries. Antimicrobial therapy is the only commercially available measure to control and prevent Brachyspira-related colitis. However, data on antimicrobial susceptibility trends and genetic diversity of Brachyspira species from North America is limited. We evaluated the antimicrobial susceptibility profiles of U.S. Brachyspira isolates recovered between 2013 and 2022 to tiamulin, tylvalosin, lincomycin, doxycycline, bacitracin, and tylosin. In addition, we performed multilocus sequence typing (MLST) on 64 B. hyodysenteriae isolates. Overall, no distinct alterations in the susceptibility patterns over time were observed among Brachyspira species. However, resistance to the commonly used antimicrobials was seen sporadically with a higher resistance frequency to tylosin compared to other tested drugs. B. hampsonii was more susceptible to the tested drugs than B. hyodysenteriae and B. pilosicoli. MLST revealed 16 different sequence types (STs) among the 64 B. hyodysenteriae isolates tested, of which 5 STs were previously known, whereas 11 were novel. Most isolates belonged to the known STs: ST93 (n = 32) and ST107 (n = 13). Our findings indicate an overall low prevalence of resistance to clinically important antimicrobials other than tylosin and bacitracin, and high genetic diversity among the clinical Brachyspira isolates from pigs in the United States during the past decade. Further molecular, epidemiologic, and surveillance studies are needed to better understand the infection dynamics of Brachyspira on swine farms and to help develop effective control measures.
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Affiliation(s)
- Maria Hakimi
- Departments of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA
| | - Fangshu Ye
- Statistics, Iowa State University, Ames, IA, USA
| | - Chloe C. Stinman
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, IA, USA
| | - Orhan Sahin
- Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA
| | - Eric R. Burrough
- Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA
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Sánchez-Busó L, Sánchez-Serrano A, Golparian D, Unemo M. pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections. Microb Genom 2024; 10:001189. [PMID: 38288762 PMCID: PMC10868605 DOI: 10.1099/mgen.0.001189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/01/2024] Open
Abstract
Extensive gonococcal surveillance has been performed using molecular typing at global, regional, national and local levels. The three main genotyping schemes for this pathogen, multi-locus sequence typing (MLST), Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR), allow inter-laboratory and inter-study comparability and reproducibility and provide an approximation to the gonococcal population structure. With whole-genome sequencing (WGS), we obtain a substantially higher and more accurate discrimination between strains compared to previous molecular typing schemes. However, WGS remains unavailable or not affordable in many laboratories, and thus bioinformatic tools that allow the integration of data among laboratories with and without access to WGS are imperative for a joint effort to increase our understanding of global pathogen threats. Here, we present pyngoST, a command-line Python tool for fast, simultaneous and accurate sequence typing of N. gonorrhoeae from WGS assemblies. pyngoST integrates MLST, NG-MAST and NG-STAR, and can also designate NG-STAR clonal complexes, NG-MAST genogroups and penA mosaicism, facilitating multiple sequence typing from large WGS assembly collections. Exact and closest matches for existing alleles and sequence types are reported. The implementation of a fast multi-pattern searching algorithm allows pyngoST to be rapid and report results on 500 WGS assemblies in under 1 min. The mapping of typing results on a core genome tree of 2375 gonococcal genomes revealed that NG-STAR is the scheme that best represents the population structure of this pathogen, emphasizing the role of antimicrobial use and antimicrobial resistance as a driver of gonococcal evolution. This article contains data hosted by Microreact.
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Affiliation(s)
- Leonor Sánchez-Busó
- Joint Research Unit ‘Infection and Public Health’, FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBERESP, ISCIII, Spain
| | - Andrea Sánchez-Serrano
- Joint Research Unit ‘Infection and Public Health’, FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Institute for Global Health, University College London (UCL), London, UK
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235
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Borrow R, Findlow J. The important lessons lurking in the history of meningococcal epidemiology. Expert Rev Vaccines 2024; 23:445-462. [PMID: 38517733 DOI: 10.1080/14760584.2024.2329618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 03/08/2024] [Indexed: 03/24/2024]
Abstract
INTRODUCTION The epidemiology of invasive meningococcal disease (IMD), a rare but potentially fatal illness, is typically described as unpredictable and subject to sporadic outbreaks. AREAS COVERED Meningococcal epidemiology and vaccine use during the last ~ 200 years are examined within the context of meningococcal characterization and classification to guide future IMD prevention efforts. EXPERT OPINION Historical and contemporary data highlight the dynamic nature of meningococcal epidemiology, with continued emergence of hyperinvasive clones and affected regions. Recent shifts include global increases in serogroup W disease, meningococcal antimicrobial resistance (AMR), and meningococcal urethritis; additionally, unvaccinated populations have experienced disease resurgences following lifting of COVID-19 restrictions. Despite these changes, a close analysis of meningococcal epidemiology indicates consistent dominance of serogroups A, B, C, W, and Y and elevated IMD rates among infants and young children, adolescents/young adults, and older adults. Demonstrably effective vaccines against all 5 major disease-causing serogroups are available, and their prophylactic use represents a powerful weapon against IMD, including AMR. The World Health Organization's goal of defeating meningitis by the year 2030 demands broad protection against IMD, which in turn indicates an urgent need to expand meningococcal vaccination programs across major disease-causing serogroups and age-related risk groups.
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Affiliation(s)
- Ray Borrow
- Meningococcal Reference Unit, UKHSA, Manchester Royal Infirmary, Manchester, UK
| | - Jamie Findlow
- Global Medical Affairs, Vaccines and Antivirals, Pfizer Ltd, Tadworth, UK
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Abdullahi IN, Latorre-Fernández J, Reuben RC, Trabelsi I, González-Azcona C, Arfaoui A, Usman Y, Lozano C, Zarazaga M, Torres C. Beyond the Wild MRSA: Genetic Features and Phylogenomic Review of mecC-Mediated Methicillin Resistance in Non- aureus Staphylococci and Mammaliicocci. Microorganisms 2023; 12:66. [PMID: 38257893 PMCID: PMC10818522 DOI: 10.3390/microorganisms12010066] [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: 12/05/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Methicillin resistance, mediated by the mecA gene in staphylococci and mammaliicocci, has caused tremendous setbacks in the use of antibiotics in human and veterinary medicine due to its high potential of presenting the multidrug resistance (MDR) phenotype. Three other mec analogs exist, of which the mecC has evolutionary been associated with methicillin-resistant Staphylococcus aureus (MRSA) in wild animals, thus loosely referred to as the wild MRSA. In this study, we present an epidemiological review and genomic analysis of non-aureus staphylococci and mammaliicocci that carry the mecC-mediated methicillin resistance trait and determine whether this trait has any relevant link with the One Health niches. All previous studies (2007 till 2023) that described the mecC gene in non-aureus staphylococci and mammaliicocci were obtained from bibliometric databases, reviewed, and systematically analyzed to obtain the antimicrobial resistance (AMR) and virulence determinants, mobilome, and other genetic contents. Moreover, core genome single-nucleotide polymorphism analysis was used to assess the relatedness of these strains. Of the 533 articles analyzed, only 16 studies (on livestock, environmental samples, milk bulk tanks, and wild animals) were eligible for inclusion, of which 17 genomes from 6 studies were used for various in silico genetic analyses. Findings from this systematic review show that all mecC-carrying non-aureus staphylococci were resistant to only beta-lactam antibiotics and associated with the classical SCCmec XI of S. aureusLGA251. Similarly, two studies on wild animals reported mecC-carrying Mammaliicoccus stepanovicii associated with SCCmec XI. Nevertheless, most of the mecC-carrying Mammaliicoccus species presented an MDR phenotype (including linezolid) and carried the SCCmec-mecC hybrid associated with mecA. The phylogenetic analysis of the 17 genomes revealed close relatedness (<20 SNPs) and potential transmission of M. sciuri and M. lentus strains in livestock farms in Algeria, Tunisia, and Brazil. Furthermore, closely related M. sciuri strains from Austria, Brazil, and Tunisia (<40 SNPs) were identified. This systematic review enhances our comprehension of the epidemiology and genetic organization of mecC within the non-aureus staphylococci and mammaliicocci. It could be hypothesized that the mecC-carrying non-aureus staphylococci are evolutionarily related to the wild MRSA-mecC. The potential implications of clonal development of a lineage of mecA/mecC carrying strains across multiple dairy farms in a vast geographical region with the dissemination of MDR phenotype is envisaged. It was observed that most mecC-carrying non-aureus staphylococci and mammaliicocci were reported in mastitis cases. Therefore, veterinarians and veterinary microbiology laboratories must remain vigilant regarding the potential existence of mecA/mecC strains originating from mastitis as a potential niche for this resistance trait.
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Affiliation(s)
- Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Javier Latorre-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Rine Christopher Reuben
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Islem Trabelsi
- Bioresources, Environment and Biotechnology Laboratory, Higher Institute of Applied Biological Sciences of Tunis, University of Tunis El Manar, Tunis 1006, Tunisia;
| | - Carmen González-Azcona
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Ameni Arfaoui
- Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1068, Tunisia;
| | - Yahaya Usman
- Department of Medical Laboratory Science, Ahmadu Bello University, Zaria 810107, Nigeria;
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
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Cranmer KD, Pant MD, Quesnel S, Sharp JA. Clonal Diversity, Antibiotic Resistance, and Virulence Factor Prevalence of Community Associated Staphylococcus aureus in Southeastern Virginia. Pathogens 2023; 13:25. [PMID: 38251333 PMCID: PMC10821353 DOI: 10.3390/pathogens13010025] [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: 11/18/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
Staphylococcus aureus is a significant human pathogen with a formidable propensity for antibiotic resistance. Worldwide, it is the leading cause of skin and soft tissue infections (SSTI), septic arthritis, osteomyelitis, and infective endocarditis originating from both community- and healthcare-associated settings. Although often grouped by methicillin resistance, both methicillin-resistant (MRSA) and methicillin-sensitive (MSSA) strains are known to cause significant pathologies and injuries. Virulence factors and growing resistance to antibiotics play major roles in the pathogenicity of community-associated strains. In our study, we examined the genetic variability and acquired antibiograms of 122 S. aureus clinical isolates from SSTI, blood, and urinary tract infections originating from pediatric patients within the southeast region of Virginia, USA. We identified a suite of clinically relevant virulence factors and evaluated their prevalence within these isolates. Five genes (clfA, spA, sbi, scpA, and vwb) with immune-evasive functions were identified in all isolates. MRSA isolates had a greater propensity to be resistant to more antibiotics as well as significantly more likely to carry several virulence factors compared to MSSA strains. Further, the carriage of various genes was found to vary significantly based on the infection type (SSTI, blood, urine).
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Affiliation(s)
- Katelyn D. Cranmer
- Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Mohan D. Pant
- School of Health Professions, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Suzanne Quesnel
- Children’s Hospital of the King’s Daughters, Norfolk, VA 23507, USA
| | - Julia A. Sharp
- Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
- School of Health Professions, Eastern Virginia Medical School, Norfolk, VA 23507, USA
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238
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Alba P, Caprioli A, Cocumelli C, Eleni C, Diaconu EL, Donati V, Ianzano A, Sorbara L, Stravino F, Cerini N, Boniotti MB, Zanoni M, Franco A, Battisti A. Genomics insights into a Mycobacterium pinnipedii isolate causing tuberculosis in a captive South American sea lion ( Otaria flavescens) from Italy. Front Microbiol 2023; 14:1303682. [PMID: 38188565 PMCID: PMC10768177 DOI: 10.3389/fmicb.2023.1303682] [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: 09/28/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Tuberculosis (TB) affects humans and other animals, and it is caused by bacteria within the Mycobacterium tuberculosis complex (MTBC). In this study, we report the characterisation of Mycobacterium pinnipedii that caused a TB case in a sea lion (Otaria flavescens) kept in an Italian zoo. The animal died due to severe, progressive disorders involving the respiratory and gastro-enteric systems and the skin. At necropsy, typical gross lesions referable to a TB generalised form were found. In particular, nodular granulomatous lesions were detected in the lungs and several lymph nodes, and colonies referable to Mycobacterium spp. were isolated from lung, mesenteric, and mediastinal lymph nodes. The isolate was identified by PCR as a MTBC, had a spoligotype SB 1480 ("seal lineage"), and was characterised and characterised by whole-genome sequencing analysis confirming that the MTBC involved was M. pinnipedii. The analysis of the resistome and virulome indicated the presence of macrolide and aminoglycoside resistance genes intrinsic in M. tuberculosis [erm-37 and aac(2')-Ic] and confirmed the presence of the region of difference 1 (RD1), harbouring the esxA and esxB virulence genes, differently from its closest taxon, M. microti. As for other MTCB members, M. pinnipedii infection can spill over into non-pinniped mammalian species; therefore, zoological gardens, veterinary practitioners, and public health officers should be aware of the hazard posed by tuberculosis from marine mammals. Since the isolate under study, as well as all available genomes of M. pinnipedii investigated in this study retains almost all the M. tuberculosis virulence genes, it could indeed cause infection, lesions, and disease in other animal species, including humans.
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Affiliation(s)
- Patricia Alba
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Andrea Caprioli
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Cristiano Cocumelli
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Claudia Eleni
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Elena Lavinia Diaconu
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Valentina Donati
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Angela Ianzano
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Luigi Sorbara
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Fiorentino Stravino
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Natalino Cerini
- Azienda Sanitaria Locale Roma 6, Servizi Veterinari, Rome, Italy
| | | | - Mariagrazia Zanoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, Brescia, Italy
| | - Alessia Franco
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Antonio Battisti
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
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Xue H, Li J, Ma L, Yang X, Ren L, Zhao Z, Wang J, Zhao Y, Zhao Z, Zhang X, Liu Z, Li Z. Seroprevalence and Molecular Characterization of Brucella abortus from the Himalayan Marmot in Qinghai, China. Infect Drug Resist 2023; 16:7721-7734. [PMID: 38144222 PMCID: PMC10749113 DOI: 10.2147/idr.s436950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 12/26/2023] Open
Abstract
Objective Brucellosis is a serious public health issue in Qinghai (QH), China. Surveying the seroprevalence and isolation of B. abortus strains from marmots is key to understanding the role of wildlife in the maintenance and spread of brucellosis. Methods In this study, a set of methods, including a serology survey, bacteriology, antibiotic susceptibility, molecular genotyping (MLST and MLVA), and genome sequencing, were employed to characterize the two B. abortus strains. Results The seroprevalence of brucellosis in marmots was 7.0% (80/1146) by serum tube agglutination test (SAT); one Brucella strain was recovered from these positive samples, and another Brucella strain from a human. Two strains were identified as B. abortus bv. 1 and were susceptible to all eight drugs examined. The distribution patterns of the accessory genes, virulence associated genes, and resistance genes of the two strains were consistent, and there was excellent collinearity between the two strains on chromosome I, but they had significant SVs in chromosome II, including inversions and translocations. MLST genotyping identified two B. abortus strains as ST2, and MLVA-16 analysis showed that the two strains clustered with strains from northern China. WGS-SNP phylogenetic analysis showed that the strains were genetically homogeneous with strains from the northern region, implying that strains from a common lineage were spread continuously in different regions and hosts. Conclusion Seroprevalence and molecular clues demonstrated frequent direct or indirect contact between sheep/goats, cattle, and marmots, implying that wildlife plays a vital role in the maintenance and spread of B. abortus in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Hongmei Xue
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Jiquan Li
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Li Ma
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Xuxin Yang
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Lingling Ren
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Zhijun Zhao
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Jianling Wang
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Yuanbo Zhao
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Zhongzhi Zhao
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Xuefei Zhang
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Zhiguo Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Zhenjun Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
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240
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Zhu L, Ji X, Wu Y, Xu W, Wang F, Huang X. Molecular characterization of Listeria monocytogenes strains isolated from imported food in China from 14 countries/regions, 2003-2018. Front Cell Infect Microbiol 2023; 13:1287564. [PMID: 38179422 PMCID: PMC10765603 DOI: 10.3389/fcimb.2023.1287564] [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: 09/02/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
Listeria monocytogenes (Lm) is associated with severe foodborne infections and ubiquitous in the nature. Identification of characteristics of Lm transmission through trading of food products is essential for rapidly tracking Lm sources and controlling dissemination of listeriosis. In this study, a total of 44 Lm strains were isolated from food products originating from 14 countries/regions during 2003-2018 at the Shanghai port. The genomes of these Lm strains were sequenced by high-throughput sequencing. Multilocus sequence typing (MLST) analysis showed that 43 isolates were divided into 17 sequence types (STs). The distribution of STs was decentralized, with the dominant ST2 accounting for only 18.18% of the strains. The LM63 strain did not match with any of the existing STs. Core-genome MLST (cgMLST) analysis based on 1748 core genes categorized the 44 strains into 30 cgMLST types (CTs), with CT10153 and CT7892 as the most predominant CTs. Notably, LM63 and LM67 shared the same CT in the cgMLST analysis. The phylogenetic analysis based on single-copy homologous genes revealed that the 44 Lm strains were primarily classified into two lineages. The SNP analysis also indicated that these strains were roughly divided into two clades, with strains in the first clade mainly collected earlier than those in the second clade, which were predominantly collected from 2010 onwards. The analysis using the virulence factor database (VFDB) indicated that the virulence gene inlJ was the most prevalent among these 44 strains. Notably, ddrA, msbA, and sugC were enriched in this dataset, requiring further clarification of their roles in Listeria through future studies. These results might provide a clue for understanding of the global epidemiology and surveillance of Lm and present insights for implementing effective measures to reduce or prevent Listeria contamination outbreaks in imported food products.
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Affiliation(s)
- Liying Zhu
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) and Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xuejiao Ji
- Shanghai Clinical Research Center for Infectious Disease (tuberculosis), Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuan Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) and Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) and Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Feifei Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) and Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xinxin Huang
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai, China
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241
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Yee WX, Elsener T, Cehovin A, Maiden MCJ, Tang CM. Evolution and exchange of plasmids in pathogenic Neisseria. mSphere 2023; 8:e0044123. [PMID: 37850911 PMCID: PMC10732060 DOI: 10.1128/msphere.00441-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/07/2023] [Indexed: 10/19/2023] Open
Abstract
IMPORTANCE Horizontal gene transfer (HGT) is a major influence in driving the spread of antimicrobial resistance (AMR) in many bacteria. A conjugative plasmid which is widespread in Neisseria gonorrhoeae, pConj, prevented the use of tetracycline/doxycycline for treating gonococcal infection. Here, we show that pConj evolved in the related pathogen, Neisseria meningitidis, and has been acquired by the gonococcus from the meningococcus on multiple occasions. Following its initial acquisition, pConj spread to different gonococcal lineages; changes in the plasmid's conjugation machinery associated with another transfer event limit spread in the gonococcal populations. Our findings have important implications for the use of doxycycline to prevent bacterial sexually transmitted disease which is likely to exacerbate the spread of AMR through HGT in pathogenic bacteria.
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Affiliation(s)
- Wearn-Xin Yee
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Tabea Elsener
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Ana Cehovin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Christoph M. Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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242
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Efron A, Biolchi A, Sorhouet Pereira C, Tomei S, Campos J, De Belder D, Moscoloni MA, Santos M, Vidal G, Nocita F, Vizzotti C, Pizza M. Bactericidal killing of meningococcal W strains isolated in Argentina by the sera of adolescents and infants immunized with 4-component meningococcal serogroup B vaccine (4CMenB). Hum Vaccin Immunother 2023; 19:2288389. [PMID: 38111094 PMCID: PMC10732599 DOI: 10.1080/21645515.2023.2288389] [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: 07/04/2023] [Accepted: 11/23/2023] [Indexed: 12/20/2023] Open
Abstract
Invasive meningococcal disease (IMD) is a life-threatening disease caused by meningococcal serogroups A, B, C, W, X, and Y, of which B and W are most common in Argentina. The 4-component meningococcal serogroup B (4CMenB) vaccine contains three purified recombinant protein antigens (Neisseria adhesin A [NadA], factor H binding protein [fHbp], and Neisserial Heparin Binding Antigen [NHBA]) and outer membrane vesicles (OMV), which is derived from the New Zealand epidemic strain and contains Porin A 1.4. These antigens are present and conserved in strains that belong to other serogroups. In this study, we show that 10/11 (91%) meningococcal serogroup W (MenW) strains selected to be representative of MenW isolates that caused IMD in Argentina during 2010-2011 were killed in bactericidal assays by the sera of adolescents and infants who had been immunized with the 4CMenB vaccine. We also show that MenW strains that caused IMD in Argentina during 2018-2021 were genetically similar to the earlier strains, indicating that the 4CMenB vaccine would likely still provide protection against current MenW strains. These data highlight the potential of 4CMenB vaccination to protect adolescents and infants against MenW strains that are endemic in Argentina.
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Affiliation(s)
- Adriana Efron
- Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Argentina
| | | | | | | | - Josefina Campos
- Centro Nacional de Genómica y Bioinformática-ANLIS “Dr. Carlos G. Malbrán”, Argentina
| | - Denise De Belder
- Centro Nacional de Genómica y Bioinformática-ANLIS “Dr. Carlos G. Malbrán”, Argentina
| | | | - Mauricio Santos
- Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Argentina
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243
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Schüler MA, Daniel R, Poehlein A. Complete genome sequence of a Clostridioides difficile cryptic C-III strain isolated from horse feces. Microbiol Resour Announc 2023; 12:e0078123. [PMID: 37909717 PMCID: PMC10720495 DOI: 10.1128/mra.00781-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
We provide the complete genome of a non-toxigenic Clostridioides difficile strain isolated from horse feces. The strain represents a sub-cluster in the cryptic clade C-III. The genome consists of one chromosome (4,144,784 bp) and one plasmid (10,144 bp) and encodes 3,798 putative genes.
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Affiliation(s)
- Miriam Antonia Schüler
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
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244
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Lerminiaux N, Mitchell R, Bartoszko J, Davis I, Ellis C, Fakharuddin K, Hota SS, Katz K, Kibsey P, Leis JA, Longtin Y, McGeer A, Minion J, Mulvey M, Musto S, Rajda E, Smith SW, Srigley JA, Suh KN, Thampi N, Tomlinson J, Wong T, Mataseje L. Plasmid genomic epidemiology of blaKPC carbapenemase-producing Enterobacterales in Canada, 2010-2021. Antimicrob Agents Chemother 2023; 67:e0086023. [PMID: 37971242 PMCID: PMC10720558 DOI: 10.1128/aac.00860-23] [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: 06/30/2023] [Accepted: 10/07/2023] [Indexed: 11/19/2023] Open
Abstract
Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. Klebsiella pneumoniae carbapenemase (blaKPC) is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn4401 transposon. This means that alongside clonal expansion, blaKPC can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 blaKPC carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular blaKPC-encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian blaKPC-encoding plasmids. We further estimated the genomic location of incomplete blaKPC-encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in K. pneumoniae clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in Enterobacter hormaechei ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of blaKPC genomic loci and indicate that multiple, distinct plasmid clusters have contributed to blaKPC spread and persistence in Canada.
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Affiliation(s)
| | | | | | - Ian Davis
- QEII Health Sciences Centre, Halifax, Nova Scotia, Canada
| | - Chelsey Ellis
- The Moncton Hospital, Moncton, New Brunswick, Canada
| | - Ken Fakharuddin
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Susy S. Hota
- University Health Network, Toronto, Ontario, Canada
| | - Kevin Katz
- North York General Hospital, Toronto, Ontario, Canada
| | - Pamela Kibsey
- Royal Jubilee Hospital, Victoria, British Columbia, Canada
| | - Jerome A. Leis
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Yves Longtin
- Jewish General Hospital, Montréal, Québec, Canada
| | | | - Jessica Minion
- Saskatchewan Health Authority, Regina, Saskatchewan, Canada
| | - Michael Mulvey
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Sonja Musto
- Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - Ewa Rajda
- McGill University Health Centre, Montréal, Québec, Canada
| | | | - Jocelyn A. Srigley
- BC Women’s and BC Children’s Hospital, Vancouver, British Columbia, Canada
| | | | - Nisha Thampi
- Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Titus Wong
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Laura Mataseje
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - on behalf of the Canadian Nosocomial Infection Surveillance Program
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
- Public Health Agency of Canada, Ottawa, Ontario, Canada
- QEII Health Sciences Centre, Halifax, Nova Scotia, Canada
- The Moncton Hospital, Moncton, New Brunswick, Canada
- University Health Network, Toronto, Ontario, Canada
- North York General Hospital, Toronto, Ontario, Canada
- Royal Jubilee Hospital, Victoria, British Columbia, Canada
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Jewish General Hospital, Montréal, Québec, Canada
- Sinai Health, Toronto, Ontario, Canada
- Saskatchewan Health Authority, Regina, Saskatchewan, Canada
- Health Sciences Centre, Winnipeg, Manitoba, Canada
- McGill University Health Centre, Montréal, Québec, Canada
- University of Alberta Hospital, Edmonton, Alberta, Canada
- BC Women’s and BC Children’s Hospital, Vancouver, British Columbia, Canada
- The Ottawa Hospital, Ottawa, Ontario, Canada
- Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
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245
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Jauregui R, Barcelo A, Bennett P, Foxwell J, Buckle K, O'Connell J, Busby B, McCulley M. Complete genomes of Pasteurella multocida isolates from porcine, bovine, and cervine samples found in New Zealand farms. Microbiol Resour Announc 2023; 12:e0088423. [PMID: 37991357 PMCID: PMC10720517 DOI: 10.1128/mra.00884-23] [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: 09/18/2023] [Accepted: 10/13/2023] [Indexed: 11/23/2023] Open
Abstract
Here, we present complete genome assemblies of Pasteurella multocida strains isolated from porcine, bovine, and cervine farms as part of bacteriology incursion investigations to identify pathogens that might present a sanitary risk to New Zealand.
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Affiliation(s)
- Ruy Jauregui
- Animal Health Laboratory, Biosecurity New Zealand, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - Andrea Barcelo
- Animal Health Laboratory, Biosecurity New Zealand, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - Peter Bennett
- Animal Health Laboratory, Biosecurity New Zealand, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - Jonathan Foxwell
- Animal Health Laboratory, Biosecurity New Zealand, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - Kelly Buckle
- Animal Health Laboratory, Biosecurity New Zealand, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - John O'Connell
- Animal Health Laboratory, Biosecurity New Zealand, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - Bede Busby
- Animal Health Laboratory, Biosecurity New Zealand, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - Michelle McCulley
- Animal Health Laboratory, Biosecurity New Zealand, Ministry for Primary Industries, Upper Hutt, New Zealand
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246
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Chaguza C, Pöntinen AK, Top J, Arredondo-Alonso S, Freitas AR, Novais C, Torres C, Bentley SD, Peixe L, Coque TM, Willems RJL, Corander J. The population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection. Microbiol Spectr 2023; 11:e0020123. [PMID: 37811975 PMCID: PMC10714801 DOI: 10.1128/spectrum.00201-23] [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: 01/13/2023] [Accepted: 08/29/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Enterococcus faecalis causes life-threatening invasive hospital- and community-associated infections that are usually associated with multidrug resistance globally. Although E. faecalis infections cause opportunistic infections typically associated with antibiotic use, immunocompromised immune status, and other factors, they also possess an arsenal of virulence factors crucial for their pathogenicity. Despite this, the relative contribution of these virulence factors and other genetic changes to the pathogenicity of E. faecalis strains remain poorly understood. Here, we investigated whether specific genomic changes in the genome of E. faecalis isolates influence its pathogenicity-infection of hospitalized and nonhospitalized individuals and the propensity to cause extraintestinal infection and intestinal colonization. Our findings indicate that E. faecalis genetics partially influence the infection of hospitalized and nonhospitalized individuals and the propensity to cause extraintestinal infection, possibly due to gut-to-bloodstream translocation, highlighting the potential substantial role of host and environmental factors, including gut microbiota, on the opportunistic pathogenic lifestyle of this bacterium.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Anna K. Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sergio Arredondo-Alonso
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ana R. Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- TOXRUN, Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carmen Torres
- Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Luisa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jukka Corander
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
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247
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Valenza G, Eisenberger D, Voigtländer S, Alsalameh R, Gerlach R, Koch S, Kunz B, Held J, Bogdan C. Emergence of novel ST1299 vanA lineages as possible cause for the striking rise of vancomycin resistance among invasive strains of Enterococcus faecium at a German university hospital. Microbiol Spectr 2023; 11:e0296223. [PMID: 37905844 PMCID: PMC10848474 DOI: 10.1128/spectrum.02962-23] [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: 09/14/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE The proportion of VREfm among all Enterococcus faecium isolated from blood cultures in German hospitals has increased in the period 2015-2020 from 11.9% to 22.3% with a country-wide spread of the clonal lineage ST117/CT71 vanB. In this study, we provided useful information about the genetic diversity of invasive strains of E. faecium. Moreover, our findings confirm the nosocomial spread of novel ST1299 vanA lineages, which recently had a rapid expansion in Austria and the south-eastern part of Germany.
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Affiliation(s)
- Giuseppe Valenza
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - David Eisenberger
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Erlangen, Germany
| | - Sven Voigtländer
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Erlangen, Germany
| | - Rayya Alsalameh
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Roman Gerlach
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Sonja Koch
- Apotheke des Universitätsklinikums Erlangen, Erlangen, Germany
| | - Bernd Kunz
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Jürgen Held
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Christian Bogdan
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
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248
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Odih EE, Sunmonu GT, Okeke IN, Dalsgaard A. NDM-1- and OXA-23-producing Acinetobacter baumannii in wastewater of a Nigerian hospital. Microbiol Spectr 2023; 11:e0238123. [PMID: 37796014 PMCID: PMC10714947 DOI: 10.1128/spectrum.02381-23] [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: 07/05/2023] [Accepted: 08/22/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Acinetobacter baumannii is a leading cause of hospital-associated infections globally. A. baumannii reservoirs outside hospital settings are still unknown, and their occurrence in the environment is linked to clinical and anthropogenic activities. Although the risk of transmission of A. baumannii from environmental sources to humans is not fully understood, these sources pose significant risks for the continued dissemination of A. baumannii and their resistance traits. This study provides evidence that diverse and clinically relevant A. baumannii strains, many of which are resistant to carbapenems, are constantly being discharged into the environment through inadequately treated hospital wastewater. We further elucidate potential transmission routes between the environment and clinical infections and demonstrate the high prevalence of carbapenem resistance genes on highly mobile transposons among these strains. Our findings highlight the pressing need to address hospital wastewater as a crucial factor in curtailing the spread of carbapenem-resistant A. baumannii.
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Affiliation(s)
- Erkison Ewomazino Odih
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Gabriel Temitope Sunmonu
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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249
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Chen YY, Chi H, Liao WC, Li SW, Yang YC, Lin HC, Chang HP, Pan YJ, Chiang RL, Hsieh YC. Genomic analysis of penicillin-binding proteins and recombination events in an emerging amoxicillin- and meropenem-resistant PMEN3 (Spain 9V-3, ST156) variant in Taiwan and comparison with global descendants of this lineage. Microbiol Spectr 2023; 11:e0184023. [PMID: 37930013 PMCID: PMC10715136 DOI: 10.1128/spectrum.01840-23] [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: 05/02/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
From 2008 to 2020, the Taiwan National Notifiable Disease Surveillance System database demonstrated that the incidence of non-vaccine serotype 23A invasive pneumococcal disease (IPD) approximately doubled. In this study, 276 non-repetitive pneumococcal clinical isolates were collected from two medical centers in Taiwan between 2019 and 2021. Of these 267 pneumococci, 60 were serotype 23A. Among them, 50 (83%) of serotype 23A isolates belonged to the sequence type (ST) 166 variant of the Spain9V-3 clone. Pneumococcal 23A-ST166 isolates were collected to assess their evolutionary relationships using whole-genome sequencing. All 23A-ST166 isolates were resistant to amoxicillin and meropenem, and 96% harbored a novel combination of penicillin-binding proteins (PBPs) (1a:2b:2x):15:11:299, the newly identified PBP2x-299 in Taiwan. Transformation of the pbp1a, pbp2b, and pbp2x alleles into the β-lactam-susceptible R6 strain revealed that PBP2x-299 and PBP2b-11 increased the MIC of ceftriaxone and meropenem by 16-fold, respectively. Prediction analysis of recombination sites in PMEN3 descendants (23A-ST166 in Taiwan, 35B-ST156 in the United States, and 11A-ST838/ST6521 in Europe) showed that adaptive evolution involved repeated, selectively favored convergent recombination in the capsular polysaccharide synthesis region, PBPs, murM, and folP genome sites. In the late 13-valent pneumococcal conjugate vaccine era, PMEN3 continuously displayed an evolutionary capacity for global dissemination and persistence, increasing IPD incidence, leading to an offset in the decrease of pneumococcal conjugate vaccine serotype-related diseases, and contributing to high antibiotic resistance. A clonal shift with a highly β-lactam-resistant non-vaccine serotype 23A, from ST338 to ST166, increased in Taiwan. ST166 is a single-locus variant of the Spain9V-3 clone, which is also called the PMEN3 lineage. All 23A-ST166 isolates, in this study, were resistant to amoxicillin and meropenem, and 96% harbored a novel combination of penicillin-binding proteins (PBPs) (1a:2b:2x):15:11:299. PBP2x-299 and PBP2b-11 contributed to the increasing MIC of ceftriaxone and meropenem, respectively. Prediction analysis of recombination sites in PMEN3 descendants showed that adaptive evolution involved repeated, selectively favored convergent recombination in the capsular polysaccharide synthesis region, PBPs, murM, and folP genome sites. In the late 13-valent pneumococcal conjugate vaccine era, PMEN3 continuously displays the evolutionary capacity for dissemination, leading to an offset in the decrease of pneumococcal conjugate vaccine serotype-related diseases and contributing to high antibiotic resistance.
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Affiliation(s)
- Yi-Yin Chen
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Hsin Chi
- Department of Medicine, MacKay Medicine College, New Taipei, Taiwan
- Department of Pediatrics, MacKay Children’s Hospital and MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wei-Chao Liao
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Shiao-Wen Li
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Yu-Ching Yang
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Ho-Chen Lin
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Hsiao-Pei Chang
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Yi-Jiun Pan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Ruei-Lin Chiang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Chia Hsieh
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
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250
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Ha EJ, Hong SM, Kim SJ, Ahn SM, Kim HW, Choi KS, Kwon HJ. Tracing the Evolutionary Pathways of Serogroup O78 Avian Pathogenic Escherichia coli. Antibiotics (Basel) 2023; 12:1714. [PMID: 38136748 PMCID: PMC10740950 DOI: 10.3390/antibiotics12121714] [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: 09/27/2023] [Revised: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Avian pathogenic E. coli (APEC) causes severe economic losses in the poultry industry, and O78 serogroup APEC strains are prevalent in chickens. In this study, we aimed to understand the evolutionary pathways and relationships between O78 APEC and other E. coli strains. To trace these evolutionary pathways, we classified 3101 E. coli strains into 306 subgenotypes according to the numbers and types of single nucleotide polymorphisms (RST0 to RST63-1) relative to the consensus sequence (RST0) of the RNA polymerase beta subunit gene and performed network analysis. The E. coli strains showed four apparently different evolutionary pathways (I-1, I-2, I-3, and II). The thirty-two Korean O78 APEC strains tested in this study were classified into RST4-4 (45.2%), RST3-1 (32.3%), RST21-1 (12.9%), RST4-5 (3.2%), RST5-1 (3.2%), and RST12-6 (3.2%), and all RSTs except RST21-1 (I-2) may have evolved through the same evolutionary pathway (I-1). A comparative genomic study revealed the highest relatedness between O78 strains of the same RST in terms of genome sequence coverage/identity and the spacer sequences of CRISPRs. The early-appearing RST3-1 and RST4-4 prevalence among O78 APEC strains may reflect the early settlement of O78 E. coli in chickens, after which these bacteria accumulated virulence and antibiotic resistance genes to become APEC strains. The zoonotic risk of the conventional O78 APEC strains is low at present, but the appearance of genetically distinct and multiple virulence gene-bearing RST21-1 O78 APEC strains may alert us to a need to evaluate their virulence in chickens as well as their zoonotic risk.
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Affiliation(s)
- Eun-Jin Ha
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Seung-Min Hong
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Seung-Ji Kim
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Sun-Min Ahn
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Ho-Won Kim
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Hyuk-Joon Kwon
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
- Laboratory of Poultry Medicine, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea
- Farm Animal Clinical Training and Research Center (FACTRC), GBST, Seoul National University, Pyeongchang 25354, Republic of Korea
- GeNiner Inc., Seoul 08826, Republic of Korea
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