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Buysse M, Koual R, Binetruy F, de Thoisy B, Baudrimont X, Garnier S, Douine M, Chevillon C, Delsuc F, Catzeflis F, Bouchon D, Duron O. Detection of Anaplasma and Ehrlichia bacteria in humans, wildlife, and ticks in the Amazon rainforest. Nat Commun 2024; 15:3988. [PMID: 38734682 PMCID: PMC11088697 DOI: 10.1038/s41467-024-48459-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Tick-borne bacteria of the genera Ehrlichia and Anaplasma cause several emerging human infectious diseases worldwide. In this study, we conduct an extensive survey for Ehrlichia and Anaplasma infections in the rainforests of the Amazon biome of French Guiana. Through molecular genetics and metagenomics reconstruction, we observe a high indigenous biodiversity of infections circulating among humans, wildlife, and ticks inhabiting these ecosystems. Molecular typing identifies these infections as highly endemic, with a majority of new strains and putative species specific to French Guiana. They are detected in unusual rainforest wild animals, suggesting they have distinctive sylvatic transmission cycles. They also present potential health hazards, as revealed by the detection of Candidatus Anaplasma sparouinense in human red blood cells and that of a new close relative of the human pathogen Ehrlichia ewingii, Candidatus Ehrlichia cajennense, in the tick species that most frequently bite humans in South America. The genome assembly of three new putative species obtained from human, sloth, and tick metagenomes further reveals the presence of major homologs of Ehrlichia and Anaplasma virulence factors. These observations converge to classify health hazards associated with Ehrlichia and Anaplasma infections in the Amazon biome as distinct from those in the Northern Hemisphere.
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Affiliation(s)
- Marie Buysse
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Rachid Koual
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Florian Binetruy
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Benoit de Thoisy
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de Guyane, Cayenne, France
- Association Kwata 'Study and Conservation of Guianan Wildlife', Cayenne, France
| | - Xavier Baudrimont
- Direction Générale des Territoires et de la Mer (DGTM) - Direction de l'environnement, de l'agriculture, de l'alimentation et de la forêt (DEAAF), Cayenne, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 uB/CNRS/EPHE, Université Bourgogne Franche-Comté, Dijon, France
| | - Maylis Douine
- Centre d'Investigation Clinique Antilles-Guyane, INSERM 1424, Centre Hospitalier de Cayenne, Cayenne, France
| | | | - Frédéric Delsuc
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - François Catzeflis
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Didier Bouchon
- EBI, University of Poitiers, UMR CNRS 7267, Poitiers, France
| | - Olivier Duron
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France.
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2
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Nong Y, Steinig E, Pollock GL, Taiaroa G, Carter GP, Monk IR, Pang S, Daley DA, Coombs GW, Forde BM, Harris PNA, Sherry NL, Howden BP, Pasricha S, Baines SL, Williamson DA. Emergence and clonal expansion of a qacA-harbouring sequence type 45 lineage of methicillin-resistant Staphylococcus aureus. Commun Biol 2024; 7:349. [PMID: 38514781 PMCID: PMC10957945 DOI: 10.1038/s42003-024-06012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
The past decade has seen an increase in the prevalence of sequence type (ST) 45 methicillin-resistant Staphylococcus aureus (MRSA), yet the underlying drivers for its emergence and spread remain unclear. To better understand the worldwide dissemination of ST45 S. aureus, we performed phylogenetic analyses of Australian isolates, supplemented with a global population of ST45 S. aureus genomes. Our analyses revealed a distinct lineage of multidrug-resistant ST45 MRSA harbouring qacA, predominantly found in Australia and Singapore. Bayesian inference predicted that the acquisition of qacA occurred in the late 1990s. qacA was integrated into a structurally variable region of the chromosome containing Tn552 (carrying blaZ) and Tn4001 (carrying aac(6')-aph(2")) transposable elements. Using mutagenesis and in vitro assays, we provide phenotypic evidence that qacA confers tolerance to chlorhexidine. These findings collectively suggest both antimicrobial resistance and the carriage of qacA may play a role in the successful establishment of ST45 MRSA.
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Affiliation(s)
- Yi Nong
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Eike Steinig
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Georgina L Pollock
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Glen P Carter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Doherty Applied Microbial Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Stanley Pang
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Denise A Daley
- Australian Group on Antimicrobial Resistance, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Brian M Forde
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
| | - Patrick N A Harris
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Norelle L Sherry
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Shivani Pasricha
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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3
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Hu F, Pan Y, Li H, Han R, Liu X, Ma R, Wu Y, Lun H, Qin X, Li J, Wang A, Zhou M, Liu B, Zhou Z, He P. Carbapenem-resistant Klebsiella pneumoniae capsular types, antibiotic resistance and virulence factors in China: a longitudinal, multi-centre study. Nat Microbiol 2024; 9:814-829. [PMID: 38424289 PMCID: PMC10914598 DOI: 10.1038/s41564-024-01612-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 01/18/2024] [Indexed: 03/02/2024]
Abstract
Epidemiological knowledge of circulating carbapenem-resistant Klebsiella pneumoniae (CRKP) is needed to develop effective strategies against this public health threat. Here we present a longitudinal analysis of 1,017 CRKP isolates recovered from patients from 40 hospitals across China between 2016 and 2020. Virulence gene and capsule typing revealed expansion of CRKP capsule type KL64 (59.5%) alongside decreases in KL47 prevalence. Hypervirulent CRKP increased in prevalence from 28.2% in 2016 to 45.7% in 2020. Phylogenetic and spatiotemporal analysis revealed Beijing and Shanghai as transmission hubs accounting for differential geographical prevalence of KL47 and KL64 strains across China. Moderate frequency capsule or O-antigen loss was also detected among isolates. Non-capsular CRKP were more susceptible to phagocytosis, attenuated during mouse infections, but showed increased serum resistance and biofilm formation. These findings give insight into CRKP serotype prevalence and dynamics, revealing the importance of monitoring serotype shifts for the future development of immunological strategies against CRKP infections.
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Affiliation(s)
- Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Yuqing Pan
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Heng Li
- Key Laboratory of Alkene-carbon Fibers-based Technology & Application for Detection of Major Infectious Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, China
| | - Renru Han
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiao Liu
- Key Laboratory of Alkene-carbon Fibers-based Technology & Application for Detection of Major Infectious Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, China
| | - Ruijing Ma
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongqin Wu
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Heyuan Lun
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohua Qin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiayin Li
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aixi Wang
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bing Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhemin Zhou
- Key Laboratory of Alkene-carbon Fibers-based Technology & Application for Detection of Major Infectious Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, China.
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Ping He
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- NHC Key Laboratory of Parasite and Vector Biology, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China.
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4
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Lee KY, Atwill ER, Li X, Feldmann HR, Williams DR, Weimer BC, Aly SS. Impact of zinc supplementation on phenotypic antimicrobial resistance of fecal commensal bacteria from pre-weaned dairy calves. Sci Rep 2024; 14:4448. [PMID: 38396015 PMCID: PMC10891156 DOI: 10.1038/s41598-024-54738-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
The objective of this study was to evaluate the impact of dietary zinc supplementation in pre-weaned dairy calves on the phenotypic antimicrobial resistance (AMR) of fecal commensal bacteria. A repository of fecal specimens from a random sample of calves block-randomized into placebo (n = 39) and zinc sulfate (n = 28) groups collected over a zinc supplementation clinical trial at the onset of calf diarrhea, calf diarrheal cure, and the last day of 14 cumulative days of zinc or placebo treatment were analyzed. Antimicrobial susceptibility testing was conducted for Enterococcus spp. (n = 167) and E. coli (n = 44), with one representative isolate of each commensal bacteria tested per sample. Parametric survival interval regression models were constructed to evaluate the association between zinc treatment and phenotypic AMR, with exponentiated accelerated failure time (AFT) coefficients adapted for MIC instead of time representing the degree of change in AMR (MIC Ratio, MR). Findings from our study indicated that zinc supplementation did not significantly alter the MIC in Enterococcus spp. for 13 drugs: gentamicin, vancomycin, ciprofloxacin, erythromycin, penicillin, nitrofurantoin, linezolid, quinupristin/dalfopristin, tylosin tartrate, streptomycin, daptomycin, chloramphenicol, and tigecycline (MR = 0.96-2.94, p > 0.05). In E. coli, zinc supplementation was not associated with resistance to azithromycin (MR = 0.80, p > 0.05) and ceftriaxone (MR = 0.95, p > 0.05). However, a significant reduction in E. coli MIC values was observed for ciprofloxacin (MR = 0.17, 95% CI 0.03-0.97) and nalidixic acid (MR = 0.28, 95% CI 0.15-0.53) for zinc-treated compared to placebo-treated calves. Alongside predictions of MIC values generated from these 17 AFT models, findings from this study corroborate the influence of age and antimicrobial exposure on phenotypic AMR.
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Affiliation(s)
- Katie Y Lee
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Edward R Atwill
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Xunde Li
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Hillary R Feldmann
- Veterinary Medicine Teaching and Research Center, University of California Davis, Tulare, CA, USA
| | - Deniece R Williams
- Veterinary Medicine Teaching and Research Center, University of California Davis, Tulare, CA, USA
| | - Bart C Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Sharif S Aly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA.
- Veterinary Medicine Teaching and Research Center, University of California Davis, Tulare, CA, USA.
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5
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Lehmkuhl J, Schneider JS, Werth KLV, Scherff N, Mellmann A, Kampmeier S. Role of membrane vesicles in the transmission of vancomycin resistance in Enterococcus faecium. Sci Rep 2024; 14:1895. [PMID: 38253607 PMCID: PMC10803344 DOI: 10.1038/s41598-024-52310-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Clonal transmission and horizontal gene transfer (HGT) contribute to the spread of vancomycin-resistant enterococci (VRE) in global healthcare. Our study investigated vesiduction, a HGT mechanism via membrane vesicles (MVs), for vanA and vanB genes that determine vancomycin resistance. We isolated MVs for VRE of different sequence types (STs) and analysed them by nanoparticle tracking analysis. Selected MV samples were subjected to DNA sequence analysis. In resistance transfer experiments, vancomycin-susceptible enterococci were exposed to MVs and bacterial supernatants of VRE. Compared to bacteria grown in lysogeny broth (MVs/LB), cultivation under vancomycin stress (MVs/VAN) resulted in increased particle concentrations of up to 139-fold (ST80). As a key finding, we could show that VRE isolates of ST80 and ST117 produced remarkably more vesicles at subinhibitory antibiotic concentrations (approx. 9.2 × 1011 particles/ml for ST80 and 2.4 × 1011 particles/ml for ST117) than enterococci of other STs (range between 1.8 × 1010 and 5.3 × 1010 particles/ml). In those MV samples, the respective resistance genes vanA and vanB were completely verifiable using sequence analysis. Nevertheless, no vancomycin resistance transfer via MVs to vancomycin-susceptible Enterococcus faecium was phenotypically detectable. However, our results outline the potential of future research on ST-specific MV properties, promising new insights into VRE mechanisms.
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Affiliation(s)
- Johanna Lehmkuhl
- Institute of Hygiene, University Hospital Münster, 48149, Münster, Germany
| | | | | | - Natalie Scherff
- Institute of Hygiene, University Hospital Münster, 48149, Münster, Germany
| | - Alexander Mellmann
- Institute of Hygiene, University Hospital Münster, 48149, Münster, Germany
| | - Stefanie Kampmeier
- Institute of Hygiene, University Hospital Münster, 48149, Münster, Germany.
- Institute for Hygiene and Microbiology, University of Würzburg, 97080, Würzburg, Germany.
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6
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Ahmad F, Javed K, Tahir A, Khan MUG, Abbas M, Rabbani M, Shabbir MZ. Identifying key soil characteristics for Francisella tularensis classification with optimized Machine learning models. Sci Rep 2024; 14:1743. [PMID: 38242908 PMCID: PMC10799052 DOI: 10.1038/s41598-024-51502-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024] Open
Abstract
Francisella tularensis (Ft) poses a significant threat to both animal and human populations, given its potential as a bioweapon. Current research on the classification of this pathogen and its relationship with soil physical-chemical characteristics often relies on traditional statistical methods. In this study, we leverage advanced machine learning models to enhance the prediction of epidemiological models for soil-based microbes. Our model employs a two-stage feature ranking process to identify crucial soil attributes and hyperparameter optimization for accurate pathogen classification using a unique soil attribute dataset. Optimization involves various classification algorithms, including Support Vector Machines (SVM), Ensemble Models (EM), and Neural Networks (NN), utilizing Bayesian and Random search techniques. Results indicate the significance of soil features such as clay, nitrogen, soluble salts, silt, organic matter, and zinc , while identifying the least significant ones as potassium, calcium, copper, sodium, iron, and phosphorus. Bayesian optimization yields the best results, achieving an accuracy of 86.5% for SVM, 81.8% for EM, and 83.8% for NN. Notably, SVM emerges as the top-performing classifier, with an accuracy of 86.5% for both Bayesian and Random Search optimizations. The insights gained from employing machine learning techniques enhance our understanding of the environmental factors influencing Ft's persistence in soil. This, in turn, reduces the risk of false classifications, contributing to better pandemic control and mitigating socio-economic impacts on communities.
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Affiliation(s)
- Fareed Ahmad
- Department of Computer Science, University of Engineering and Technology, Lahore, Pakistan.
- Quality Operations Laboratory, Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
| | - Kashif Javed
- Department of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Ahsen Tahir
- Department of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | | | - Mateen Abbas
- Quality Operations Laboratory, Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Masood Rabbani
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Zubair Shabbir
- Quality Operations Laboratory, Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
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Ba X, Guo Y, Moran RA, Doughty EL, Liu B, Yao L, Li J, He N, Shen S, Li Y, van Schaik W, McNally A, Holmes MA, Zhuo C. Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone. Nat Commun 2024; 15:494. [PMID: 38216585 PMCID: PMC10786849 DOI: 10.1038/s41467-023-43854-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/22/2023] [Indexed: 01/14/2024] Open
Abstract
Carbapenem-resistant Escherichia coli (CREC) ST410 has recently emerged as a major global health problem. Here, we report a shift in CREC prevalence in Chinese hospitals between 2017 and 2021 with ST410 becoming the most commonly isolated sequence type. Genomic analysis identifies a hypervirulent CREC ST410 clone, B5/H24RxC, which caused two separate outbreaks in a children's hospital. It may have emerged from the previously characterised B4/H24RxC in 2006 and has been isolated in ten other countries from 2015 to 2021. Compared with B4/H24RxC, B5/H24RxC lacks the blaOXA-181-bearing X3 plasmid, but carries a F-type plasmid containing blaNDM-5. Most of B5/H24RxC also carry a high pathogenicity island and a novel O-antigen gene cluster. We find that B5/H24RxC grew faster in vitro and is more virulent in vivo. The identification of this newly emerged but already globally disseminated hypervirulent CREC clone, highlights the ongoing evolution of ST410 towards increased resistance and virulence.
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Affiliation(s)
- Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yingyi Guo
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Robert A Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Emma L Doughty
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Baomo Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Likang Yao
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiahui Li
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Nanhao He
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Siquan Shen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Yang Li
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
| | - Chao Zhuo
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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8
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Khalili P, Tevell S, Fischer P, Hailer NP, Wolf O. Analysis of fracture-related infections from Swedish insurance claims between 2011 and 2021. Sci Rep 2023; 13:22662. [PMID: 38114785 PMCID: PMC10730616 DOI: 10.1038/s41598-023-50224-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/16/2023] [Indexed: 12/21/2023] Open
Abstract
Fracture-related infections (FRI) pose a serious complication with an incidence of 1-2%. This study aimed to analyze compensation claims submitted to The Swedish National Patient Insurance Company (LÖF) because of FRI after closed/open reduction and internal fixation (C/ORIF) in the four most common fracture sites (proximal humerus, distal radius, hip, ankle). Patients registered in the LÖF database with a suspected FRI between 2011 and 2021 were identified by matching International Classification of Diseases and procedural codes indicative of a combination of fractures to the proximal humerus, distal radius, hip and ankle, C/ORIF and infection. Medical records were reviewed for fracture sites, pathogens and complications. Data from the Swedish Fracture Register (SFR) were extracted to estimate the proportion of reported claims to the presumed number of FRI. Of 122 FRI identified in the LÖF database, 34 were after C/ORIF in the proximal humerus, 12 in the distal radius, 28 in the hip and 48 in the ankle. LÖF compensated 111 patients (91%). Median time from C/ORIF to an FRI was 3 weeks (interquartile range 2-6), and 95% of all FRI occurred within 1 year after C/ORIF. Staphylococcus aureus was the most common pathogen in patients with a distal radius, hip and ankle FRI. In contrast, Cutibacterium spp. were the most common aetiology in FRI of the proximal humerus. The total number of fractures treated with C/ORIF in the four fracture sites registered in the SFR during 2021 was 18,711. Most of the FRI patients were diagnosed within the first year after C/ORIF, and 91% of the patients received compensation. Given an expected FRI incidence of 1-2%, our estimates with extrapolated data from the SFR indicate that < 10% of affected patients applied for compensation.
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Affiliation(s)
- Pendar Khalili
- Department of Surgical Sciences, Orthopedics, Uppsala University, Uppsala, Sweden.
- Department of Orthopedic Surgery, Karlstad Hospital, Rosenborgsgatan 9, 652 30, Karlstad, Sweden.
- Centre for Clinical Research and Education, Region Värmland, Karlstad, Sweden.
| | - Staffan Tevell
- Centre for Clinical Research and Education, Region Värmland, Karlstad, Sweden
- Department of Infectious Diseases, Karlstad Hospital, Karlstad, Sweden
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Per Fischer
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Nils P Hailer
- Department of Surgical Sciences, Orthopedics, Uppsala University, Uppsala, Sweden
| | - Olof Wolf
- Department of Surgical Sciences, Orthopedics, Uppsala University, Uppsala, Sweden
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9
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Zhong L, Zhang M, Sun L, Yang Y, Wang B, Yang H, Shen Q, Xia Y, Cui J, Hang H, Ren Y, Pang B, Deng X, Zhan Y, Li H, Zhou Z. Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century. Nat Commun 2023; 14:7706. [PMID: 38001084 PMCID: PMC10673917 DOI: 10.1038/s41467-023-43528-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Core genome multilocus sequence typing (cgMLST) is commonly used to classify bacterial strains into different types, for taxonomical and epidemiological applications. However, cgMLST schemes require central databases for the nomenclature of new alleles and sequence types, which must be synchronized worldwide and involve increasingly intensive calculation and storage demands. Here, we describe a distributed cgMLST (dcgMLST) scheme that does not require a central database of allelic sequences and apply it to study evolutionary patterns of epidemic and endemic strains of the genus Neisseria. We classify 69,994 worldwide Neisseria strains into multi-level clusters that assign species, lineages, and local disease outbreaks. We divide Neisseria meningitidis into 168 endemic lineages and three epidemic lineages responsible for at least 9 epidemics in the past century. According to our analyses, the epidemic and endemic lineages experienced very different population dynamics in the past 100 years. Epidemic lineages repetitively emerged from endemic lineages, disseminated worldwide, and apparently disappeared rapidly afterward. We propose a stepwise model for the evolutionary trajectory of epidemic lineages in Neisseria, and expect that the development of similar dcgMLST schemes will facilitate epidemiological studies of other bacterial pathogens.
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Affiliation(s)
- Ling Zhong
- Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, 215123, China
- Key Laboratory of Alkene-Carbon Fibers-Based Technology & Application for Detection of Major Infectious Diseases, Soochow University, Suzhou, 215123, China
| | - Menghan Zhang
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Libing Sun
- Department of Pathology, East District of Suzhou Municipal Hospital, Suzhou, 215000, China
| | - Yu Yang
- Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, 215123, China
| | - Bo Wang
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Haibing Yang
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Qiang Shen
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Yu Xia
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Jiarui Cui
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Hui Hang
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Yi Ren
- Iotabiome Biotechnology Inc, Suzhou, 215000, China
| | - Bo Pang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiangyu Deng
- Center for Food Safety, University of Georgia, Griffin, GA, USA
| | - Yahui Zhan
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China.
| | - Heng Li
- Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, 215123, China.
- Key Laboratory of Alkene-Carbon Fibers-Based Technology & Application for Detection of Major Infectious Diseases, Soochow University, Suzhou, 215123, China.
- Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Soochow University, Suzhou, 215123, China.
| | - Zhemin Zhou
- Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, 215123, China.
- Key Laboratory of Alkene-Carbon Fibers-Based Technology & Application for Detection of Major Infectious Diseases, Soochow University, Suzhou, 215123, China.
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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10
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Stenhouse GE, Keddy KH, Bengtsson RJ, Hall N, Smith AM, Thomas J, Iturriza-Gómara M, Baker KS. The genomic epidemiology of shigellosis in South Africa. Nat Commun 2023; 14:7715. [PMID: 38001075 PMCID: PMC10673971 DOI: 10.1038/s41467-023-43345-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.
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Affiliation(s)
- George E Stenhouse
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK.
| | | | - Rebecca J Bengtsson
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Miren Iturriza-Gómara
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Kate S Baker
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK.
- Department of Genetics, University of Cambridge, CB23EH, Cambridge, UK.
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11
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Akoko JM, Mwatondo A, Muturi M, Wambua L, Abkallo HM, Nyamota R, Bosire C, Oloo S, Limbaso KS, Gakuya F, Nthiwa D, Bartlow A, Middlebrook E, Fair J, Ogutu JO, Gachohi J, Njenga K, Bett B. Mapping brucellosis risk in Kenya and its implications for control strategies in sub-Saharan Africa. Sci Rep 2023; 13:20192. [PMID: 37980384 PMCID: PMC10657468 DOI: 10.1038/s41598-023-47628-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/16/2023] [Indexed: 11/20/2023] Open
Abstract
In Sub-Saharan Africa (SSA), effective brucellosis control is limited, in part, by the lack of long-term commitments by governments to control the disease and the absence of reliable national human and livestock population-based data to inform policies. Therefore, we conducted a study to establish the national prevalence and develop a risk map for Brucella spp. in cattle to contribute to plans to eliminate the disease in Kenya by the year 2040. We randomly generated 268 geolocations and distributed them across Kenya, proportionate to the area of each of the five agroecological zones and the associated cattle population. Cattle herds closest to each selected geolocation were identified for sampling. Up to 25 cattle were sampled per geolocation and a semi-structured questionnaire was administered to their owners. We tested 6,593 cattle samples for Brucella immunoglobulin G (IgG) antibodies using an Enzyme-linked immunosorbent assay (ELISA). We assessed potential risk factors and performed spatial analyses and prevalence mapping using approximate Bayesian inference implemented via the integrated nested Laplace approximation (INLA) method. The national Brucella spp. prevalence was 6.8% (95% CI: 6.2-7.4%). Exposure levels varied significantly between agro-ecological zones, with a high of 8.5% in the very arid zone with the lowest agricultural potential relative to a low of 0.0% in the agro-alpine zone with the highest agricultural potential. Additionally, seroprevalence increased with herd size, and the odds of seropositivity were significantly higher for females and adult animals than for males or calves. Similarly, animals with a history of abortion, or with multiple reproductive syndromes had higher seropositivity than those without. At the herd level, the risk of Brucella spp. transmission was higher in larger herds, and herds with a history of reproductive problems such as abortion, giving birth to weak calves, or having swollen testes. Geographic localities with high Brucella seroprevalence occurred in northern, eastern, and southern regions of Kenya all primarily characterized by semi-arid or arid agro-ecological zones dominated by livestock pastoralism interspersed with vast areas with mixed livestock-wildlife systems. The large spatial extent of our survey provides compelling evidence for the widespread geographical distribution of brucellosis risk across Kenya in a manner easily understandable for policymakers. Our findings can provide a basis for risk-stratified pilot studies aiming to investigate the cost-effectiveness and efficacy of singular and combined preventive intervention strategies that seek to inform Kenya's Brucellosis Control Policy.
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Affiliation(s)
- James M Akoko
- International Livestock Research Institute, Nairobi, Kenya.
| | - Athman Mwatondo
- International Livestock Research Institute, Nairobi, Kenya
- Zoonotic Disease Unit, Nairobi, Kenya
- Department of Medical Microbiology and Immunology, Faculty of Health, University of Nairobi, Nairobi, Kenya
| | - Mathew Muturi
- International Livestock Research Institute, Nairobi, Kenya
- Zoonotic Disease Unit, Nairobi, Kenya
- Faculty of Veterinary Medicine, Dahlem Research School of Biomedical Sciences, Freie Universität Berlin, Berlin, Germany
| | - Lillian Wambua
- International Livestock Research Institute, Nairobi, Kenya
- World Organisation for Animal Health, Sub-Regional Representation for Eastern Africa, Nairobi, Kenya
| | | | | | | | - Stephen Oloo
- International Livestock Research Institute, Nairobi, Kenya
| | | | - Francis Gakuya
- Wildlife Research and Training Institute, Naivasha, Kenya
| | - Daniel Nthiwa
- Department of Biological Sciences, University of Embu, Embu, Kenya
| | | | | | - Jeanne Fair
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Joseph O Ogutu
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - John Gachohi
- Global Health Programme, Washington State University, Nairobi, Kenya
- School of Public Health, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
- Paul G, Allen School of Global Health, Washington State University, Pullman, WA, 99164, USA
| | - Kariuki Njenga
- Global Health Programme, Washington State University, Nairobi, Kenya
- Paul G, Allen School of Global Health, Washington State University, Pullman, WA, 99164, USA
| | - Bernard Bett
- International Livestock Research Institute, Nairobi, Kenya
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12
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El Zowalaty ME, Lamichhane B, Falgenhauer L, Mowlaboccus S, Zishiri OT, Forsythe S, Helmy YA. Antimicrobial resistance and whole genome sequencing of novel sequence types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans isolated from livestock. Sci Rep 2023; 13:18609. [PMID: 37903806 PMCID: PMC10616195 DOI: 10.1038/s41598-023-42838-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/15/2023] [Indexed: 11/01/2023] Open
Abstract
The emergence of antimicrobial-resistant, livestock-associated Enterococcus faecalis represents a public health concern. Here, we report the isolation, molecular detection of virulence and antimicrobial resistance determinants, in addition to the phylogenetic analyses of 20 Enterococcus species using whole genome sequencing analysis of 15 Enterococcus faecalis strains including six strains of three novel sequence types, three Enterococcus faecium and two Enterococcus durans. All strains were isolated from food chain animals in South Africa. Enterococcus strains were isolated on bile aesculin azide agar, followed by identification using MALDI-TOF MS analysis. Antibiotic susceptibility testing was performed using the Kirby-Bauer disk diffusion method. The genomic DNA of the isolates was extracted and sequencing was performed using the Illumina MiSeq platform. Sequence reads were trimmed and de novo assembled. The assembled contigs were analyzed for antimicrobial resistance genes and chromosomal mutations, extra-chromosomal plasmids, and multi-locus sequence type (MLST). Multidrug antimicrobial resistance genes conferring resistance to aminoglycosides (ant(6)-Ia, aph(3')-IIIa, sat4, and spw), lincosamides (lnu(B), lsa(A), and lsa(E)), macrolides (erm(B)), trimethoprim (dfrG) and tetracyclines (tet(L) and tet(M)) were identified. Plasmid replicons were detected in seven E. faecalis and three E. faecium isolates. The sequence type (ST) of each isolate was determined using the Enterococcus PubMLST database. Ten STs were identified in the collection, three of which (ST1240, ST1241, and ST1242) have not been previously reported and are described in the present study for the first time. To compare the sequenced strains to other previously sequenced E. faecalis strains, assembled sequences of E. faecalis from livestock were downloaded from the PubMLST database. Core genome-based phylogenetic analysis was performed using ParSNP. The detection of multiple drug-resistance in Enterococcus including E. faecalis and E. faecium highlights the significance of genomic surveillance to monitor the spread of antimicrobial resistance in food chain animals. In addition, the genome sequences of Enterococcus strains reported in the present study will serve as a reference point for future molecular epidemiological studies of livestock-associated and antibiotic-resistant E. faecalis in Africa. In addition, this study enables the in-depth analysis of E. faecalis genomic structure, as well as provides valuable information on the phenotypic and genotypic antimicrobial resistance, and the pathogenesis of livestock-associated E. faecalis and E. faecium.
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Affiliation(s)
- Mohamed E El Zowalaty
- Veterinary Medicine and Food Security Research Group, Medical Laboratory Sciences Program, Faculty of Health Sciences, Abu Dhabi Women's Campus, Higher Colleges of Technology, Abu Dhabi, 41012, UAE.
| | - Bibek Lamichhane
- Department of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Biomedical Research Center Seltersberg, Schubertstrasse 81, 35392, Giessen, Germany
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Oliver T Zishiri
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Private Bag X54001, Westville, Durban, 4000, South Africa
| | - Stephen Forsythe
- Foodmicrobe.com Ltd., Adams Hill, Keyworth, Nottingham, NG12 5GY, UK
| | - Yosra A Helmy
- Department of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, 40546, USA.
- Department of Zoonoses, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt.
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13
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Jonaitis P, Nyssen OP, Saracino IM, Fiorini G, Vaira D, Pérez-Aísa Á, Tepes B, Castro-Fernandez M, Pabón-Carrasco M, Keco-Huerga A, Voynovan I, Lucendo AJ, Lanas Á, Martínez-Domínguez SJ, Almajano EA, Rodrigo L, Vologzanina L, Brglez Jurecic N, Denkovski M, Bujanda L, Mahmudov U, Leja M, Lerang F, Babayeva G, Bordin DS, Gasbarrini A, Kupcinskas J, Gridnyev O, Rokkas T, Marcos-Pinto R, Phull PS, Smith SM, Tonkić A, Boltin D, Buzás GM, Šembera Š, Şimşek H, Matysiak-Budnik T, Milivojevic V, Marlicz W, Venerito M, Boyanova L, Doulberis M, Capelle LG, Cano-Català A, Moreira L, Mégraud F, O'Morain C, Gisbert JP, Jonaitis L. Comparison of the management of Helicobacter pylori infection between the older and younger European populations. Sci Rep 2023; 13:17235. [PMID: 37821503 PMCID: PMC10567783 DOI: 10.1038/s41598-023-43287-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023] Open
Abstract
The prevalence of Helicobacter pylori remains high in the older population. Specific age-related peculiarities may impact the outcomes of H. pylori treatment. The aim of the study was to evaluate the diagnostics and effectiveness of H. pylori eradication between the younger and older European populations. "European Registry on H. pylori Management (Hp-EuReg)" data from 2013 to 2022 were analyzed. Patients were divided into older (≥ 60 years) and younger (18-59 years) groups. Modified intention-to-treat (mITT) and per-protocol (PP) analysis was performed. 49,461 patients included of which 14,467 (29%) were older-aged. Concomitant medications and penicillin allergy were more frequent among the older patients. Differences between younger and older populations were observed in treatment duration in first-line treatment and in proton pump inhibitors (PPIs) doses in second-line treatment. The overall incidence of adverse events was lower in the older adults group. The overall first-line treatment mITT effectiveness was 88% in younger and 90% in the older patients (p < 0.05). The overall second-line mITT treatment effectiveness was 84% in both groups. The effectiveness of the most frequent first- and second-line triple therapies was suboptimal (< 90%) in both groups. Optimal efficacy (≥ 90%) was achieved by using bismuth and non-bismuth-based quadruple therapies. In conclusion, the approach to the diagnostics and treatment of H. pylori infection did not generally differ between younger and older patients. Main differences were reported in the concurrent medications, allergy to penicillin and adverse events both in first- and second-line treatment. Optimal effectiveness rates were mostly achieved by using bismuth and non-bismuth-based quadruple therapies. No clinically relevant differences in the effectiveness between the age groups were observed.
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Affiliation(s)
- Paulius Jonaitis
- Department of Gastroenterology, Lithuanian University of Health Sciences, 50161, Kaunas, Lithuania
| | - Olga P Nyssen
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad Autónoma de Madrid (UAM), Diego de León, 62, 28006, Madrid, Spain.
| | - Ilaria Maria Saracino
- Department of Surgical and Medical Sciences, IRCCS AOUBO, University of Bologna, 40138, Bologna, Italy
| | - Giulia Fiorini
- Department of Surgical and Medical Sciences, IRCCS AOUBO, University of Bologna, 40138, Bologna, Italy
| | - Dino Vaira
- Department of Surgical and Medical Sciences, IRCCS AOUBO, University of Bologna, 40138, Bologna, Italy
| | - Ángeles Pérez-Aísa
- Agencia Sanitaria Costa del Sol, Red de Investigación en Servicios de Salud en Enfermedades Crónicas (REDISSEC), 29651, Marbella, Spain
| | - Bojan Tepes
- Department of Gastroenterology, AM DC Rogaska, 3250, Rogaska Slatina, Slovenia
| | | | | | - Alma Keco-Huerga
- Department of Gastroenterology, Hospital de Valme, 41014, Seville, Spain
| | - Irina Voynovan
- Department of Gastroenterology, A.S. Loginov Moscow Clinical Scientific Center, 111123, Moscow, Russia
| | - Alfredo J Lucendo
- Department of Gastroenterology, Hospital General de Tomelloso, 13700, Tomelloso, Spain
| | - Ángel Lanas
- IIS Aragón y Facultad de Medicina de la Universidad de Zaragoza, 50009, Zaragoza, Spain
| | | | | | - Luis Rodrigo
- Gastroenterology Unit, Hospital Universitario Central de Asturias, 33011, Oviedo, Spain
| | | | - Natasa Brglez Jurecic
- Department of Gastroenterology, Interni Oddelek, Diagnostic Centre, 4260, Bled, Slovenia
| | - Maja Denkovski
- Department of Gastroenterology, Interni Oddelek, Diagnostic Centre, 4260, Bled, Slovenia
| | - Luis Bujanda
- Hospital Donostia, Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), 20018, San Sebastián, Spain
| | | | - Mārcis Leja
- Department of Gastroenterology, Digestive Diseases Centre Gastro, Institute of Clinical and Preventive Medicine and Faculty of Medicine, University of Latvia, Riga, 1079, Latvia
| | - Frode Lerang
- Department of Gastroenterology, Østfold Hospital Trust, 1714, Grålum, Norway
| | | | - Dmitry S Bordin
- Department of Gastroenterology, A.S. Loginov Moscow Clinical Scientific Center, 111123, Moscow, Russia
- A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473, Moscow, Russia
- Tver State Medical University, 170100, Tver, Russia
| | - Antonio Gasbarrini
- Medicina Interna, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Juozas Kupcinskas
- Department of Gastroenterology, Lithuanian University of Health Sciences, 50161, Kaunas, Lithuania
| | - Oleksiy Gridnyev
- Government Institution "L.T.Malaya Therapy National Institute of the National Academy of Medical Sciences of Ukraine", Kyiv, Ukraine
| | - Theodore Rokkas
- Department of Gastroenterology, Henry Dunant Hospital, 115 26, Athens, Greece
| | - Ricardo Marcos-Pinto
- Department of Gastroenterology, Centro Hospitalar do Porto Institute of Biomedical Sciences Abel Salazar, Centro de Investigação em Tecnologias e Serviços de Saúde, University of Porto, 4050-313, Porto, Portugal
| | - Perminder S Phull
- Department of Gastroenterology, Aberdeen Royal Infirmary, Aberdeen, AB25 2ZN, UK
| | - Sinead M Smith
- Faculty of Health Sciences, Trinity College Dublin, Dublin, D02PN40, Ireland
| | - Ante Tonkić
- Department of Gastroenterology, University Hospital of Split, University of Split School of Medicine, 21000, Split, Croatia
| | - Doron Boltin
- Division of Gastroenterology, Rabin Medical Center, Sackler School of Medicine, Tel Aviv University, 49100, Tel Aviv, Israel
| | - György Miklós Buzás
- Department of Gastroenterology, Ferencváros Health Centre, 1095, Budapest, Hungary
| | - Štěpán Šembera
- 2nd Department of Internal Medicine and Gastroenterology, University Hospital and Charles University, Faculty of Medicine in Hradec Králové, 500 03, Hradec Králové, Czech Republic
| | - Halis Şimşek
- Division of Gastroenterology and Hepatology, Hacettepe University School of Medicine, 06230, Ankara, Turkey
| | - Tamara Matysiak-Budnik
- Department of Gastroenterology, CHRU de Nantes, Hôpital Hôtel Dieu, 44000, Nantes, France
| | - Vladimir Milivojevic
- Department of Gastroenterology, Clinical Center of Serbia, University of Belgrade School of Medicine, 11000, Belgrade, Serbia
| | - Wojciech Marlicz
- Department of Gastroenterology, Pomeranian Medical University, 70-204, Szczecin, Poland
| | - Marino Venerito
- Department of Gastroenterology, Otto-Von-Guericke University, 39120, Magdeburg, Germany
| | - Lyudmila Boyanova
- Department of Gastroenterology, Medical Microbiology, Medical University of Sofia, 1431, Sofia, Bulgaria
| | - Michael Doulberis
- Division of Gastroenterology and Hepatology, Medical University Department, Kantonsspital Aarau, 5001, Aarau, Switzerland
| | - Lisette G Capelle
- Department of Gastroenterology, Meander Medical Center, 3813 TZ, Amersfoort, The Netherlands
| | - Anna Cano-Català
- GOES Research Group, Althaia Xarxa Assistencial Universitària de Manresa, 08243, Manresa, Spain
| | - Leticia Moreira
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036, Barcelona, Spain
| | - Francis Mégraud
- INSERM U1312, Université de Bordeaux, 33000, Bordeaux, France
| | - Colm O'Morain
- Faculty of Health Sciences, Trinity College Dublin, Dublin, D02PN40, Ireland
| | - Javier P Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad Autónoma de Madrid (UAM), Diego de León, 62, 28006, Madrid, Spain
| | - Laimas Jonaitis
- Department of Gastroenterology, Lithuanian University of Health Sciences, 50161, Kaunas, Lithuania
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14
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Neemuchwala A, Zittermann S, Johnson K, Middleton D, Stapleton PJ, Ravirajan V, Cronin K, Allen VG, Patel SN. Whole genome sequencing of increased number of azithromycin-resistant Shigella flexneri 1b isolates in Ontario. Sci Rep 2023; 13:16582. [PMID: 37789081 PMCID: PMC10547750 DOI: 10.1038/s41598-023-36733-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/08/2023] [Indexed: 10/05/2023] Open
Abstract
Azithromycin (AZM) resistance among Shigella is a major public health concern. Here, we investigated the epidemiology of Shigella flexneri serotype 1b recovered during 2016-2018 in Ontario, to describe the prevalence and spread of AZM resistance. We found that 72.3% (47/65) of cases were AZM-resistant (AZMR), of which 95.7% (45/47) were among males (P < 0.001). Whole-genome based phylogenetic analysis showed three major clusters, and 56.9% of isolates grouped within a single closely-related cluster (0-10 ∆SNP). A single AZMR clonal population was persistent over 3 years and involved 67.9% (36/53) of all male cases, and none reported international travel. In 2018, a different AZMR cluster appeared among adult males not reporting travel. A proportion of isolates (10.7%) with reduced susceptibility to ciprofloxacin (CIP) due to S83L mutation in gyrA were AZM susceptible, and 71.4% reported international travel. Resistance to AZM was due to the acquisition of mph gene-bearing incFII plasmids having > 95% nucleotide similarity to pKSR100. Plasmid-borne resistance limiting treatment options to AZM, ceftriaxone (CRO) and CIP was noted in a single isolate. We characterized AZMR isolates circulating locally among males and found that genomic analysis can support targeted prevention and mitigation strategies against antimicrobial-resistance.
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Affiliation(s)
- Alefiya Neemuchwala
- Ontario Agency for Health Protection and Promotion (Public Health Ontario), Toronto, ON, Canada
| | - Sandra Zittermann
- Ontario Agency for Health Protection and Promotion (Public Health Ontario), Toronto, ON, Canada
| | - Karen Johnson
- Ontario Agency for Health Protection and Promotion (Public Health Ontario), Toronto, ON, Canada
| | - Dean Middleton
- Ontario Agency for Health Protection and Promotion (Public Health Ontario), Toronto, ON, Canada
| | - Patrick J Stapleton
- Ontario Agency for Health Protection and Promotion (Public Health Ontario), Toronto, ON, Canada
| | - Vithusha Ravirajan
- Ontario Agency for Health Protection and Promotion (Public Health Ontario), Toronto, ON, Canada
| | - Kirby Cronin
- Ontario Agency for Health Protection and Promotion (Public Health Ontario), Toronto, ON, Canada
| | - Vanessa G Allen
- Ontario Agency for Health Protection and Promotion (Public Health Ontario), Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Sinai Health, Mount Sinai Hospital, Toronto, ON, Canada
| | - Samir N Patel
- Ontario Agency for Health Protection and Promotion (Public Health Ontario), Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Microbiology and Laboratory Science, Public Health Ontario, 661 University Ave, Suite 1701, Toronto, ON, M5G 1M1, Canada.
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15
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Brangsch H, Horstkotte MA, Melzer F. Genotypic peculiarities of a human brucellosis case caused by Brucella suis biovar 5. Sci Rep 2023; 13:16586. [PMID: 37789135 PMCID: PMC10547717 DOI: 10.1038/s41598-023-43570-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/26/2023] [Indexed: 10/05/2023] Open
Abstract
Human brucellosis cases are rare in non-endemic countries, such as Germany, where infections are predominantly caused by Brucella melitensis. The German National Reference Laboratory for Bovine, Porcine, Ovine and Caprine Brucellosis received a suspected Brucella sp. isolate from a patient for identification. Bacteriological tests and PCR-based diagnostics showed the isolate to be B. suis, but did not yield cohesive results regarding the biovar. Whole genome sequencing and subsequent genotyping was employed for a detailed characterization of the isolate and elucidating the reason for failure of the diagnostic PCR to correctly identify the biovar. The isolate was found to be B. suis bv. 5, a rare biovar with limited geographical distribution primarily found in the Northern Caucasus. Due to a deletion in one of the target regions of the diagnostic PCR, the isolate could not be correctly typed. Based on in silico genotyping it could be excluded that the isolate was identical to one of the B. suis bv. 5 reference strains. Here, we report a rare case of a B. suis bv. 5 field isolate. Furthermore, by reporting this finding, we want to make practitioners aware of possible misinterpretation of PCR results, as it cannot be excluded that the detected deletion is common among the B. suis bv. 5 community, as there is currently a lack of field isolates.
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Affiliation(s)
- Hanka Brangsch
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Jena, Germany.
| | | | - Falk Melzer
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Jena, Germany
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16
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Schouls LM, Witteveen S, van Santen-Verheuvel M, de Haan A, Landman F, van der Heide H, Kuijper EJ, Notermans DW, Bosch T, Hendrickx APA. Molecular characterization of MRSA collected during national surveillance between 2008 and 2019 in the Netherlands. Commun Med (Lond) 2023; 3:123. [PMID: 37700016 PMCID: PMC10497500 DOI: 10.1038/s43856-023-00348-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Although the Netherlands is a country with a low endemic level, methicillin-resistant Staphylococcus aureus (MRSA) poses a significant health care problem. Therefore, high coverage national MRSA surveillance has been in place since 1989. To monitor possible changes in the type-distribution and emergence of resistance and virulence, MRSA isolates are molecularly characterized. METHODS All 43,321 isolates from 36,520 persons, collected 2008-2019, were typed by multiple-locus variable number tandem repeats analysis (MLVA) with simultaneous PCR detection of the mecA, mecC and lukF-PV genes, indicative for PVL. Next-generation sequencing data of 4991 isolates from 4798 persons were used for whole genome multi-locus sequence typing (wgMLST) and identification of resistance and virulence genes. RESULTS We show temporal change in the molecular characteristics of the MRSA population with the proportion of PVL-positive isolates increasing from 15% in 2008-2010 to 25% in 2017-2019. In livestock-associated MRSA obtained from humans, PVL-positivity increases to 6% in 2017-2019 with isolates predominantly from regions with few pig farms. wgMLST reveals the presence of 35 genogroups with distinct resistance, virulence gene profiles and specimen origin. Typing shows prolonged persistent MRSA carriage with a mean carriage period of 407 days. There is a clear spatial and a weak temporal relationship between isolates that clustered in wgMLST, indicative for regional spread of MRSA strains. CONCLUSIONS Using molecular characterization, this exceptionally large study shows genomic changes in the MRSA population at the national level. It reveals waxing and waning of types and genogroups and an increasing proportion of PVL-positive MRSA.
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Affiliation(s)
- Leo M Schouls
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
| | - Sandra Witteveen
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Marga van Santen-Verheuvel
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Angela de Haan
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Fabian Landman
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Han van der Heide
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology and Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daan W Notermans
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Thijs Bosch
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Antoni P A Hendrickx
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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17
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Tchesnokova V, Larson L, Basova I, Sledneva Y, Choudhury D, Solyanik T, Heng J, Bonilla TC, Pham S, Schartz EM, Madziwa LT, Holden E, Weissman SJ, Ralston JD, Sokurenko EV. Increase in the community circulation of ciprofloxacin-resistant Escherichia coli despite reduction in antibiotic prescriptions. Commun Med (Lond) 2023; 3:110. [PMID: 37567971 PMCID: PMC10421857 DOI: 10.1038/s43856-023-00337-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Community circulating gut microbiota is the main reservoir for uropathogenic Escherichia coli, including those resistant to antibiotics. Ciprofloxacin had been the primary antibiotic prescribed for urinary tract infections, but its broad use has been discouraged and steadily declined since 2015. How this change in prescriptions affected the community circulation of ciprofloxacin-resistant E. coli is unknown. METHODS We determined the frequency of isolation and other characteristics of E. coli resistant to ciprofloxacin in 515 and 1604 E. coli-positive fecal samples collected in 2015 and 2021, respectively. The samples were obtained from non-antibiotic-taking women of age 50+ receiving care in the Kaiser Permanente Washington healthcare system. RESULTS Here we show that despite a nearly three-fold drop in the prescription of ciprofloxacin between 2015 and 2021, the rates of gut carriage of ciprofloxacin-resistant E. coli increased from 14.2 % to 19.8% (P = .004). This is driven by a significant increase of isolates from the pandemic multi-drug resistant clonal group ST1193 (1.7% to 4.2%; P = .009) and isolates with relatively few ciprofloxacin-resistance determining chromosomal mutations (2.3% to 7.4%; P = .00003). Though prevalence of isolates with the plasmid-associated ciprofloxacin resistance dropped (59.0% to 30.9%; P = 2.7E-06), the isolates co-resistance to third generation cephalosporins has increased from 14.1% to 31.5% (P = .002). CONCLUSIONS Despite reduction in ciprofloxacin prescriptions, community circulation of the resistant uropathogenic E. coli increased with a rise of co-resistance to third generation cephalosporins. Thus, to reduce the rates of urinary tract infections refractory to antibiotic treatment, greater focus should be on controlling the resistant bacteria in gut microbiota.
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Affiliation(s)
- Veronika Tchesnokova
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Lydia Larson
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Irina Basova
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Yulia Sledneva
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Debarati Choudhury
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Thalia Solyanik
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Jennifer Heng
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Teresa Christina Bonilla
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Sophia Pham
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Ellen M Schartz
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA, 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA, 98101-1466, USA
| | - Lawrence T Madziwa
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA, 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA, 98101-1466, USA
| | - Erika Holden
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA, 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA, 98101-1466, USA
| | - Scott J Weissman
- Department of Laboratory Medicine, Seattle Children's Hospital, 1100 Olive Way Tutor Center, Seattle, WA, 98101, USA
| | - James D Ralston
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA, 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA, 98101-1466, USA
| | - Evgeni V Sokurenko
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA.
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18
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Chen CJ, Casteriano A, Green AC, Govendir M. A retrospective study on antibacterial treatments for koalas infected with Chlamydia pecorum. Sci Rep 2023; 13:12670. [PMID: 37542093 PMCID: PMC10403558 DOI: 10.1038/s41598-023-39832-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023] Open
Abstract
Chlamydiosis remains the leading infectious disease and is one of the key factors responsible for the dramatic reduction of koala populations in South-East Queensland (SEQ) and New South Wales (NSW) regions of Australia. Possible infection outcomes include blindness, infertility, painful cystitis, and death if left untreated. Studies have reported the treatment efficacy of chloramphenicol and doxycycline, which are the two most commonly administered treatments in diseased koalas, in clinical settings. However, none have directly compared the treatment efficacy of these antibacterials on koala survival. A retrospective study was essential to identify any relationships between the demographical information, and the animals' responses to the current treatment regimens. Associations were explored between six explanatory (sex; maturity; location; clinical signs, treatment; treatment duration) and two outcome variables (survival; post-treatment PCR). Results showed that female koalas had a statistical trend of lower odds of surviving when compared to males (OR = 0.36, p = 0.05). Koalas treated with chloramphenicol for ≥ 28 days had greater odds of surviving than when treated for < 28 days (OR = 8.8, p = 0.02), and those koalas administered doxycycline had greater odds of testing PCR negative when compared to chloramphenicol treatments (OR = 5.45, p = 0.008). There was no difference between the antibacterial treatments (chloramphenicol, doxycycline, and mixed/other) and the survival of koalas. Female koalas had greater odds of exhibiting UGT signs only (OR = 4.86, p < 0.001), and also greater odds of having both ocular and UGT clinical signs (OR = 5.29, p < 0.001) when compared to males. Of the koalas, 28.5% initially had no clinical signs but were PCR positive for C. pecorum. This study enables further understanding of the complex nature between chlamydial infection and response to antibacterial treatment.
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Affiliation(s)
- Chien-Jung Chen
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia.
| | - Andrea Casteriano
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Alexandra Clare Green
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Merran Govendir
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
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19
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Huggins LG, Baydoun Z, Mab R, Khouri Y, Schunack B, Traub RJ, Colella V. Transmission of haemotropic mycoplasma in the absence of arthropod vectors within a closed population of dogs on ectoparasiticides. Sci Rep 2023; 13:10143. [PMID: 37349533 PMCID: PMC10287653 DOI: 10.1038/s41598-023-37079-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023] Open
Abstract
Dog-infecting haemotropic mycoplasmas (haemoplasmas), such as Mycoplasma haemocanis and Candidatus Mycoplasma haematoparvum are common blood-borne pathogens of canines that can potentially inflict a substantial burden of disease, particularly in immunosuppressed individuals. Nonetheless, the transmission of these pathogens remains debated as more evidence emerges that they may not be transmitted by vectors, but instead use alternative methods such as aggressive interactions and vertical transmission. Here, we treated forty dogs with two different topically-acting ectoparasiticide products able to prevent vector-borne pathogen infections during an 8-month community trial in Cambodia. A total absence of ectoparasites were observed at all time points, and no new infections caused by pathogens confirmed as being vectorially-transmitted were detected, i.e., Babesia vogeli, Ehrlichia canis, Anaplasma platys, and Hepatozoon canis. Conversely, the number of haemoplasma infections in dogs on both ectoparasiticides rose significantly, with an incidence of 26 infections per 100 dogs at risk per year, providing strong evidence of non-vectorial transmission. Over the study period, dog aggression and fighting were frequently observed, highlighting a different potential mode of transmission. This study presents the first robust evidence that canine haemoplasmas may be transmitted without arthropod vectors drawing attention to the need for new methods to prevent their transmission.
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Affiliation(s)
- Lucas G Huggins
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia.
| | - Zahida Baydoun
- Animal Mama Veterinary Hospital, Phnom Penh, 12312, Cambodia
| | - Ron Mab
- Animal Mama Veterinary Hospital, Phnom Penh, 12312, Cambodia
| | - Yulia Khouri
- Animal Mama Veterinary Hospital, Phnom Penh, 12312, Cambodia
| | | | - Rebecca J Traub
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia
| | - Vito Colella
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia.
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20
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Bah SY, Kujabi MA, Darboe S, Kebbeh N, Kebbeh BFK, Kanteh A, Bojang R, Lawn JE, Kampmann B, Sesay AK, de Silva TI, Brotherton H. Acquisition and carriage of genetically diverse multi-drug resistant gram-negative bacilli in hospitalised newborns in The Gambia. Commun Med (Lond) 2023; 3:79. [PMID: 37270610 PMCID: PMC10239441 DOI: 10.1038/s43856-023-00309-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/25/2023] [Indexed: 06/05/2023] Open
Abstract
BACKGROUND This detailed genomic study characterised multi-drug resistant-Gram negative bacilli (MDR-GNB) carriage in neonates < 2 kg and paired mothers at a low-resource African hospital. METHODS This cross-sectional cohort study was conducted at the neonatal referral unit in The Gambia with weekly neonatal skin and peri-anal sampling and paired maternal recto-vaginal swabs. Prospective bacteriological culture used MacConkey agar with species identification by API20E and API20NE. All GNB isolates underwent whole genome sequencing on Illumina Miseq platform. Multi-Locus Sequence Typing and SNP-distance analysis identified strain type and relatedness. RESULTS 135 swabs from 34 neonates and 21 paired mothers, yielded 137 GNB isolates, of which 112 are high quality de novo assemblies. Neonatal MDR-GNB carriage prevalence is 41% (14/34) at admission with 85% (11/13) new acquisition by 7d. Multiple MDR and ESBL-GNB species are carried at different timepoints, most frequently K. pneumoniae and E. coli, with heterogeneous strain diversity and no evidence of clonality. 111 distinct antibiotic resistance genes are mostly beta lactamases (Bla-AMPH, Bla-PBP, CTX-M-15, Bla-TEM-105). 76% (16/21) and 62% (13/21) of mothers have recto-vaginal carriage of ≥1 MDR-GNB and ESBL-GNB respectively, mostly MDR-E. coli (76%, 16/21) and MDR-K. pneumoniae (24%, 5/21). Of 21 newborn-mother dyads, only one have genetically identical isolates (E. coli ST131 and K. pneumoniae ST3476). CONCLUSIONS Gambian hospitalised neonates exhibit high MDR and ESBL-GNB carriage prevalence with acquisition between birth and 7d with limited evidence supporting mother to neonate transmission. Genomic studies in similar settings are required to further understand transmission and inform targeted surveillance and infection prevention policies.
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Affiliation(s)
- Saikou Y Bah
- The Florey Institute of Host-Pathogen Interactions, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
- MRC Unit, The Gambia at LSHTM, Atlantic Road, Fajara, The Gambia
| | - Mariama A Kujabi
- MRC Unit, The Gambia at LSHTM, Atlantic Road, Fajara, The Gambia
| | - Saffiatou Darboe
- MRC Unit, The Gambia at LSHTM, Atlantic Road, Fajara, The Gambia
| | - Ngange Kebbeh
- MRC Unit, The Gambia at LSHTM, Atlantic Road, Fajara, The Gambia
| | - Bunja F K Kebbeh
- MRC Unit, The Gambia at LSHTM, Atlantic Road, Fajara, The Gambia
| | - Abdoulie Kanteh
- MRC Unit, The Gambia at LSHTM, Atlantic Road, Fajara, The Gambia
| | | | - Joy E Lawn
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology & Population Health London School of Hygiene & Tropical Medicine, London, UK
| | - Beate Kampmann
- MRC Unit, The Gambia at LSHTM, Atlantic Road, Fajara, The Gambia
- Department of Clinical Research, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Institut fur Internationale Gesundheit and Centre for Global Health, Charite Universitatsmedizin, Berlin, Germany
| | - Abdul K Sesay
- MRC Unit, The Gambia at LSHTM, Atlantic Road, Fajara, The Gambia
| | - Thushan I de Silva
- The Florey Institute of Host-Pathogen Interactions, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
- MRC Unit, The Gambia at LSHTM, Atlantic Road, Fajara, The Gambia
| | - Helen Brotherton
- MRC Unit, The Gambia at LSHTM, Atlantic Road, Fajara, The Gambia.
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology & Population Health London School of Hygiene & Tropical Medicine, London, UK.
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21
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Guo X, Yan M, Huang D, Chen S, Zhang D, Li Z, Yang X, Wu W. A large scale 16S ribosomal RNA gene amplicon dataset of hand, foot and mouth patients and healthy individuals. Sci Data 2023; 10:48. [PMID: 36681671 PMCID: PMC9867725 DOI: 10.1038/s41597-023-01953-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
There is evidence linking hand, foot and mouth disease (HFMD) to gut microbiota dysbiosis, and this relationship was corroborated in a large HFMD patient population in our previous study. Here, we present a bacterial 16S rRNA gene dataset from faecal samples of 713 individuals (254 HFMD patients, 459 healthy controls) aged 2 to 7 years residing in Heyuan and Jiangmen counties, Guangdong Province, southern China. Microbiome analysis indicated a significant increase in genus Prevotella, Cetobacterium, and Megamonas was observed in patients with HFMD, whereas a large increase in genus Bacteroides, Ruminococcus, and Faecalibacterium were seen in the control group. We also share the bioinformatic analytical pipeline for this analysis, from data preprocessing to data filtering and amplicon sequence variant (ASV) table generation. We expect that the dataset will be reprocessed, evaluated and fully analysed with various analysis methods to further elucidate the role of the gut microbiota in HFMD development.
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Affiliation(s)
- Xiaoying Guo
- School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Min Yan
- School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Dongyi Huang
- School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Siyi Chen
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Dantao Zhang
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Zhifeng Li
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Xingfen Yang
- School of Public Health, Southern Medical University, Guangzhou, China.
| | - Wei Wu
- School of Public Health, Southern Medical University, Guangzhou, China.
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
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22
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Hilton B, Wilson DJ, O'Connell AM, Ironmonger D, Rudkin JK, Allen N, Oliver I, Wyllie DH. Laboratory diagnosed microbial infection in English UK Biobank participants in comparison to the general population. Sci Rep 2023; 13:496. [PMID: 36627297 PMCID: PMC9831014 DOI: 10.1038/s41598-022-20635-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/15/2022] [Indexed: 01/11/2023] Open
Abstract
Understanding the genetic and environmental risk factors for serious bacterial infections in ageing populations remains incomplete. Utilising the UK Biobank (UKB), a prospective cohort study of 500,000 adults aged 40-69 years at recruitment (2006-2010), can help address this. Partial implementation of such a system helped groups around the world make rapid progress understanding risk factors for SARS-CoV-2 infection and COVID-19, with insights appearing as early as May 2020. In principle, such approaches could also to be used for bacterial isolations. Here we report feasibility testing of linking an England-wide dataset of microbial reporting to UKB participants, to enable characterisation of microbial infections within the UKB Cohort. These records pertain mainly to bacterial isolations; SARS-CoV-2 isolations were not included. Microbiological infections occurring in patients in England, as recorded in the Public Health England second generation surveillance system (SGSS), were linked to UKB participants using pseudonymised identifiers. By January 2015, ascertainment of laboratory reports from UKB participants by SGSS was estimated at 98%. 4.5% of English UKB participants had a positive microbiological isolate in 2015. Half of UKB isolates came from 12 laboratories, and 70% from 21 laboratories. Incidence rate ratios for microbial isolation, which is indicative of serious infection, from the UKB cohort relative to the comparably aged general population ranged from 0.6 to 1, compatible with the previously described healthy participant bias in UKB. Data on microbial isolations can be linked to UKB participants from January 2015 onwards. This linked data would offer new opportunities for research into the role of bacterial agents on health and disease in middle to-old age.
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Affiliation(s)
| | - Daniel J Wilson
- Nuffield Department of Population Health, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | | | | | - Justine K Rudkin
- Nuffield Department of Population Health, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Naomi Allen
- Nuffield Department of Population Health, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | | | - David H Wyllie
- UK Health Security Agency, London, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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23
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Ahmad F, Ghani Khan MU, Tahir A, Tipu MY, Rabbani M, Shabbir MZ. Two phase feature-ranking for new soil dataset for Coxiella burnetii persistence and classification using machine learning models. Sci Rep 2023; 13:29. [PMID: 36593267 DOI: 10.1038/s41598-022-26956-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/22/2022] [Indexed: 01/03/2023] Open
Abstract
Coxiella burnetii (Cb) is a hardy, stealth bacterial pathogen lethal for humans and animals. Its tremendous resistance to the environment, ease of propagation, and incredibly low infectious dosage make it an attractive organism for biowarfare. Current research on the classification of Coxiella and features influencing its presence in the soil is generally confined to statistical techniques. Machine learning other than traditional approaches can help us better predict epidemiological modeling for this soil-based pathogen of public significance. We developed a two-phase feature-ranking technique for the pathogen on a new soil feature dataset. The feature ranking applies methods such as ReliefF (RLF), OneR (ONR), and correlation (CR) for the first phase and a combination of techniques utilizing weighted scores to determine the final soil attribute ranks in the second phase. Different classification methods such as Support Vector Machine (SVM), Linear Discriminant Analysis (LDA), Logistic Regression (LR), and Multi-Layer Perceptron (MLP) have been utilized for the classification of soil attribute dataset for Coxiella positive and negative soils. The feature-ranking methods established that potassium, chromium, cadmium, nitrogen, organic matter, and soluble salts are the most significant attributes. At the same time, manganese, clay, phosphorous, copper, and lead are the least contributing soil features for the prevalence of the bacteria. However, potassium is the most influential feature, and manganese is the least significant soil feature. The attribute ranking using RLF generates the most promising results among the ranking methods by generating an accuracy of 80.85% for MLP, 79.79% for LR, and 79.8% for LDA. Overall, SVM and MLP are the best-performing classifiers, where SVM yields an accuracy of 82.98% and 81.91% for attribute ranking by CR and RLF; and MLP generates an accuracy of 76.60% for ONR. Thus, machine models can help us better understand the environment, assisting in the prevalence of bacteria and decreasing the chances of false classification. Subsequently, this can assist in controlling epidemics and alleviating the devastating effect on the socio-economics of society.
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Qiu S, Liu K, Yang C, Xiang Y, Min K, Zhu K, Liu H, Du X, Yang M, Wang L, Sun Y, Zhou H, Mahe M, Zhao J, Li S, Yu D, Hawkey J, Holt KE, Baker S, Yang J, Xu X, Song H. A Shigella sonnei clone with extensive drug resistance associated with waterborne outbreaks in China. Nat Commun 2022; 13:7365. [PMID: 36450777 PMCID: PMC9709761 DOI: 10.1038/s41467-022-35136-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
Abstract
Antimicrobial resistance of Shigella sonnei has become a global concern. Here, we report a phylogenetic group of S. sonnei with extensive drug resistance, including a combination of multidrug resistance, coresistance to ceftriaxone and azithromycin (cefRaziR), reduced susceptibility to fluoroquinolones, and even colistin resistance (colR). This distinct clone caused six waterborne shigellosis outbreaks in China from 2015 to 2020. We collect 155 outbreak isolates and 152 sporadic isolates. The cefRaziR isolates, including outbreak strains, are mainly distributed in a distinct clade located in global Lineage III. The outbreak strains form a recently derived monophyletic group that may have emerged circa 2010. The cefRaziR and colR phenotypes are attributed to the acquisition of different plasmids, particularly the IncB/O/K/Z plasmid coharboring the blaCTX-M-14, mphA, aac(3)-IId, dfrA17, aadA5, and sul1 genes and the IncI2 plasmid with an mcr-1 gene. Genetic analyses identify 92 accessory genes and 60 single-nucleotide polymorphisms associated with the cefRaziR phenotype. Surveillance of this clone is required to determine its dissemination and threat to global public health.
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Affiliation(s)
- Shaofu Qiu
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kangkang Liu
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Chaojie Yang
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Ying Xiang
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kaiyuan Min
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Kunpeng Zhu
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbo Liu
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xinying Du
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Mingjuan Yang
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Ligui Wang
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yong Sun
- grid.410620.10000 0004 1757 8298Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Haijian Zhou
- grid.198530.60000 0000 8803 2373National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention and State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Muti Mahe
- Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Jiayong Zhao
- grid.418504.cHenan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Shijun Li
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Deshan Yu
- grid.508057.fGansu Provincial Center for Disease Control and Prevention, Lanzhou, China
| | - Jane Hawkey
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Monash University, Melbourne, VIC Australia
| | - Kathryn E. Holt
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Monash University, Melbourne, VIC Australia
| | - Stephen Baker
- grid.5335.00000000121885934University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Juntao Yang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xuebin Xu
- grid.430328.eShanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Hongbin Song
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
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25
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Liao S, Gong G, Wang X, Tian L. Membrane damage mechanism of protocatechualdehyde against Micrococcus luteus and its effect on pork quality characteristics. Sci Rep 2022; 12:18856. [PMID: 36344587 DOI: 10.1038/s41598-022-23309-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022] Open
Abstract
This study investigated the mechanism of membrane damage by protocatechualdehyde (PCA) against Micrococcus luteus and assessed effects of PCA on the sensory and physicochemical properties of pork. The mechanism of PCA inhibition on M. luteus was studied by determining the minimum inhibitory concentration (MIC) based on membrane potential, intracellular ATP concentration, intracellular pH, confocal laser scanning microscopy (CLSM), and field emission gun scanning electron microscopy (FEG-SEM). The results showed that the MIC of PCA against M. luteus was 1.25 mg/mL. Hyperpolarization of the bacterial cell membrane, a decrease in the intracellular ATP concentration, and intracellular pH indicated that PCA damaged the cell membrane of M. luteus. FEG-SEM observation revealed that PCA could cause surface collapse, cell membrane rupture, and content outflow of M. luteus. Additionally, PCA was found to inhibit increases in the total number of colonies, the thiobarbituric acid reactive substances (TBARS) value growth rate, and moisture mobility in raw pork. Additionally, it improved the color and texture of raw pork, all of which effectively prolonged its shelf life. This study will encourage the application of PCA as a natural antibacterial agent in the food industry.
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26
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Comín J, Cebollada A, Ibarz D, Viñuelas J, Sahagún J, Torres L, Iglesias MJ, Samper S. Analysis of the twenty-six largest outbreaks of tuberculosis in Aragon using whole-genome sequencing for surveillance purposes. Sci Rep 2022; 12:18766. [PMID: 36335223 DOI: 10.1038/s41598-022-23343-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/30/2022] [Indexed: 11/08/2022] Open
Abstract
The incidence of tuberculosis in Aragon, Spain, is around ten cases per 100,000 inhabitants. Since 2004, a molecular surveillance protocol has been carried out; therefore, all M. tuberculosis strains are genotyped. Recently, whole-genome sequencing has been implemented for relevant isolates. The aim of this work is to characterise at the molecular level the causative strains of the 26 largest outbreaks of the community (including ten or more cases), genotyped by IS6110-RFLP and causing 26% of tuberculosis cases. To achieve this objective, two or three isolates of each IS6110-cluster belonging to different years were selected for sequencing. We found that strains of lineages L4.8, L4.3 and L4.1.2 were the most frequent. The threshold of 12 SNPs as the maximum distance for confirming the belonging to an outbreak was met for 18 of the 26 IS6110-clusters. Four pairs of isolates with more than 90 SNPs were identified as not belonging to the same strain, and four other pairs were kept in doubt as the number of SNPs was close to 12, between 14 and 35. The study of Regions of Difference revealed that they are lineage conserved. Moreover, we could analyse the IS6110 locations for all genome-sequenced isolates, finding some frequent locations in isolates belonging to the same lineage and certain IS6110 movements between the paired isolates. In the vast majority, these movements were not captured by the IS6110-RFLP pattern. After classifying the genes containing SNP by their functional category, we could confirm that the number of SNPs detected in genes considered as virulence factors and the number of cases the strain produced were not related, suggesting that a particular SNP is more relevant than the number. The characteristics found in the most successful strains in our community could be useful for other researchers in epidemiology, virulence and pathogenesis.
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27
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Satti I, Wittenberg RE, Li S, Harris SA, Tanner R, Cizmeci D, Jacobs A, Williams N, Mulenga H, Fletcher HA, Scriba TJ, Tameris M, Hatherill M, McShane H. Inflammation and immune activation are associated with risk of Mycobacterium tuberculosis infection in BCG-vaccinated infants. Nat Commun 2022; 13:6594. [PMID: 36329009 PMCID: PMC9632577 DOI: 10.1038/s41467-022-34061-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Tuberculosis vaccine development is hindered by the lack of validated immune correlates of protection. Exploring immune correlates of risk of disease and/or infection in prospective samples can inform this field. We investigate whether previously identified immune correlates of risk of TB disease also associate with increased risk of M.tb infection in BCG-vaccinated South African infants, who became infected with M.tb during 2-3 years of follow-up. M.tb infection is defined by conversion to positive reactivity in the QuantiFERON test. We demonstrate that inflammation and immune activation are associated with risk of M.tb infection. Ag85A-specific IgG is elevated in infants that were subsequently infected with M.tb, and this is coupled with upregulated gene expression of immunoglobulin-associated genes and type-I interferon. Plasma levels of IFN-[Formula: see text]2, TNF-[Formula: see text], CXCL10 (IP-10) and complement C2 are also higher in infants that were subsequently infected with M.tb.
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Affiliation(s)
- Iman Satti
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Rachel E Wittenberg
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Shuailin Li
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Stephanie A Harris
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Rachel Tanner
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Deniz Cizmeci
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Ashley Jacobs
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK.,Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nicola Williams
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Helen A Fletcher
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Michele Tameris
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Helen McShane
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
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28
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Larsen J, Raisen CL, Ba X, Sadgrove NJ, Padilla-González GF, Simmonds MSJ, Loncaric I, Kerschner H, Apfalter P, Hartl R, Deplano A, Vandendriessche S, Černá Bolfíková B, Hulva P, Arendrup MC, Hare RK, Barnadas C, Stegger M, Sieber RN, Skov RL, Petersen A, Angen Ø, Rasmussen SL, Espinosa-Gongora C, Aarestrup FM, Lindholm LJ, Nykäsenoja SM, Laurent F, Becker K, Walther B, Kehrenberg C, Cuny C, Layer F, Werner G, Witte W, Stamm I, Moroni P, Jørgensen HJ, de Lencastre H, Cercenado E, García-Garrote F, Börjesson S, Hæggman S, Perreten V, Teale CJ, Waller AS, Pichon B, Curran MD, Ellington MJ, Welch JJ, Peacock SJ, Seilly DJ, Morgan FJE, Parkhill J, Hadjirin NF, Lindsay JA, Holden MTG, Edwards GF, Foster G, Paterson GK, Didelot X, Holmes MA, Harrison EM, Larsen AR. Emergence of methicillin resistance predates the clinical use of antibiotics. Nature 2022; 602:135-141. [PMID: 34987223 PMCID: PMC8810379 DOI: 10.1038/s41586-021-04265-w] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022]
Abstract
The discovery of antibiotics more than 80 years ago has led to considerable improvements in human and animal health. Although antibiotic resistance in environmental bacteria is ancient, resistance in human pathogens is thought to be a modern phenomenon that is driven by the clinical use of antibiotics1. Here we show that particular lineages of methicillin-resistant Staphylococcus aureus-a notorious human pathogen-appeared in European hedgehogs in the pre-antibiotic era. Subsequently, these lineages spread within the local hedgehog populations and between hedgehogs and secondary hosts, including livestock and humans. We also demonstrate that the hedgehog dermatophyte Trichophyton erinacei produces two β-lactam antibiotics that provide a natural selective environment in which methicillin-resistant S. aureus isolates have an advantage over susceptible isolates. Together, these results suggest that methicillin resistance emerged in the pre-antibiotic era as a co-evolutionary adaptation of S. aureus to the colonization of dermatophyte-infected hedgehogs. The evolution of clinically relevant antibiotic-resistance genes in wild animals and the connectivity of natural, agricultural and human ecosystems demonstrate that the use of a One Health approach is critical for our understanding and management of antibiotic resistance, which is one of the biggest threats to global health, food security and development.
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Affiliation(s)
- Jesper Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark.
| | - Claire L Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | | | | | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Heidrun Kerschner
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Petra Apfalter
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Rainer Hartl
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Ariane Deplano
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
| | - Stien Vandendriessche
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
- Laboratory for Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavel Hulva
- Department of Zoology, Charles University, Prague, Czech Republic
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Maiken C Arendrup
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Rasmus K Hare
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Céline Barnadas
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Marc Stegger
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N Sieber
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Robert L Skov
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Andreas Petersen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Øystein Angen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sophie L Rasmussen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Wildlife Conservation Research Unit (WildCRU), Department of Zoology, University of Oxford, Tubney, UK
| | - Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Laura J Lindholm
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Frederic Laurent
- Bacteriology Department and French National Reference Center for Staphylococci, Hospices Civils de Lyon, University of Lyon, Lyon, France
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Birgit Walther
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, Berlin, Germany
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Justus-Liebig University Giessen, Giessen, Germany
| | - Christiane Cuny
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Franziska Layer
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Wolfgang Witte
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | | | - Paolo Moroni
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
- Quality Milk Production Services, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, USA
| | | | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB NOVA, Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Emilia Cercenado
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Fernando García-Garrote
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain
- Servicio de Microbiología, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain
| | - Stefan Börjesson
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Sara Hæggman
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | | | - Andrew S Waller
- Animal Health Trust, Newmarket, UK
- Intervacc AB, Stockholm, Stockholm, Sweden
- Department of Biomedical Science and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bruno Pichon
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
| | - Matthew J Ellington
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - David J Seilly
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Fiona J E Morgan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Department of Physiology, Development & Neuroscience, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nazreen F Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jodi A Lindsay
- Institute of Infection and Immunity, St George's, University of London, London, UK
| | | | - Giles F Edwards
- Scottish MRSA Reference Laboratory, NHS Greater Glasgow and Clyde, Stobhill Hospital, Glasgow, UK
| | | | - Gavin K Paterson
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Warwick, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Anders R Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
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29
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Mora-Hernández Y, Vera Murguía E, Stinenbosch J, Hernández Jauregui P, van Dijl JM, Buist G. Molecular typing and antimicrobial resistance profiling of 33 mastitis-related Staphylococcus aureus isolates from cows in the Comarca Lagunera region of Mexico. Sci Rep 2021; 11:6912. [PMID: 33767356 PMCID: PMC7994548 DOI: 10.1038/s41598-021-86453-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/10/2021] [Indexed: 11/26/2022] Open
Abstract
Mastitis in cows is a major cause of economic losses and it is commonly associated with Staphylococcus aureus. Little is known about the S. aureus lineages causing mastitis in Mexican cattle. The aim of this study was to type S. aureus isolates causing mastitis in cows from the Comarca Lagunera region in Mexico in 2015-2016. Multi-locus variable number tandem repeat fingerprinting (MLVF) of 33 S. aureus isolates obtained from 210 milk samples revealed the MLVF clusters A (n = 1), B (n = 26), C (n = 5) and D (n = 1). Spa-typing showed that clusters A and B represent the spa-type t224, cluster C includes spa-types t3196 and t416, and cluster D represents spa-type t114. The different spa-types were mirrored by the masses of protein A bands as detected by Western blotting. Antimicrobial susceptibility testing showed that one isolate was susceptible to all antimicrobials tested, whereas all other strains were resistant only to benzylpenicillin. These findings show that only four S. aureus lineages, susceptible to most antimicrobials, were responsible for causing mastitis at the time of sampling. Lastly, many isolates carried the same small plasmid, designated pSAM1. The high prevalence of pSAM1 amongst the antimicrobial-susceptible isolates suggests an association with bovine colonization or mastitis rather than antimicrobial resistance.
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Affiliation(s)
- Y Mora-Hernández
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - E Vera Murguía
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - J Stinenbosch
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | | | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.
| | - G Buist
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
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30
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Sierra-Arguello YM, Perdoncini G, Rodrigues LB, Ruschel Dos Santos L, Apellanis Borges K, Quedi Furian T, Pippi Salle CT, de Souza Moraes HL, Pereira Gomes MJ, Pinheiro do Nascimento V. Identification of pathogenic genes in Campylobacter jejuni isolated from broiler carcasses and broiler slaughterhouses. Sci Rep 2021; 11:4588. [PMID: 33633256 DOI: 10.1038/s41598-021-84149-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 02/08/2021] [Indexed: 02/08/2023] Open
Abstract
Campylobacter jejuni is one of the most common causes of foodborne diseases worldwide. There are few reports on Campylobacter strains isolated from Latin-American countries. Here, 140 C. jejuni strains isolated from cloacal and transport boxes swabs, water from chiller tanks, and broiler carcasses of five poultry companies in Southern Brazil were identified using phenotypic and genotypic methods. Polymerase chain reaction (PCR) was used to analyze eight C. jejuni virulence markers: flaA, cadF, and invasion-associated (iam) genes, cdtABC operon (associated with the cytolethal distending toxin), and plasmidial virB11 and wlaN genes were present in 78.5%, 77.8%, 0%, 74.2%, 22.1%, and 10.7% of samples, respectively. There were 25 different virulence profiles: 1 (cdtA, cdtB, cdtC, flaA, and cadF), 2 (cdtA, cdtB, cdtC, flaA, cadF, and virB11), and 3 (cdtA, cdtB, cdtC, flaA, cadF, and wlaN) were the most common (> 60% of strains). We provide insight into factors related to the occurrence of this pathogen and their epidemiology.
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31
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Argimón S, Masim MAL, Gayeta JM, Lagrada ML, Macaranas PKV, Cohen V, Limas MT, Espiritu HO, Palarca JC, Chilam J, Jamoralin MC, Villamin AS, Borlasa JB, Olorosa AM, Hernandez LFT, Boehme KD, Jeffrey B, Abudahab K, Hufano CM, Sia SB, Stelling J, Holden MTG, Aanensen DM, Carlos CC. Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines. Nat Commun 2020; 11:2719. [PMID: 32483195 PMCID: PMC7264328 DOI: 10.1038/s41467-020-16322-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022] Open
Abstract
National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can support surveillance by pinpointing resistance mechanisms and uncovering transmission patterns. However, genomic surveillance is rare in low- and middle-income countries. Here, we implement WGS within the established Antimicrobial Resistance Surveillance Program of the Philippines via a binational collaboration. In parallel, we characterize bacterial populations of key bug-drug combinations via a retrospective sequencing survey. By linking the resistance phenotypes to genomic data, we reveal the interplay of genetic lineages (strains), AMR mechanisms, and AMR vehicles underlying the expansion of specific resistance phenotypes that coincide with the growing carbapenem resistance rates observed since 2010. Our results enhance our understanding of the drivers of carbapenem resistance in the Philippines, while also serving as the genetic background to contextualize ongoing local prospective surveillance.
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Affiliation(s)
- Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
| | - Melissa A L Masim
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - June M Gayeta
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Marietta L Lagrada
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Polle K V Macaranas
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Victoria Cohen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
| | - Marilyn T Limas
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Holly O Espiritu
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Janziel C Palarca
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Jeremiah Chilam
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Manuel C Jamoralin
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Alfred S Villamin
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Janice B Borlasa
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Agnettah M Olorosa
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Lara F T Hernandez
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Karis D Boehme
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Benjamin Jeffrey
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
| | - Khalil Abudahab
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
| | - Charmian M Hufano
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
- St. Luke's Medical Center-Global City, Taguig, Metro Manila, The Philippines
| | - Sonia B Sia
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | | | | | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - Celia C Carlos
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines.
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32
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Shetty AC, Jacob CG, Huang F, Li Y, Agrawal S, Saunders DL, Lon C, Fukuda MM, Ringwald P, Ashley EA, Han KT, Hlaing TM, Nyunt MM, Silva JC, Stewart KE, Plowe CV, O'Connor TD, Takala-Harrison S. Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns. Nat Commun 2019; 10:2665. [PMID: 31209259 PMCID: PMC6572796 DOI: 10.1038/s41467-019-10121-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 04/17/2019] [Indexed: 02/08/2023] Open
Abstract
Estimates of Plasmodium falciparum migration may inform strategies for malaria elimination. Here we elucidate fine-scale parasite population structure and infer recent migration across Southeast Asia using identity-by-descent (IBD) approaches based on genome-wide single nucleotide polymorphisms called in 1722 samples from 54 districts. IBD estimates are consistent with isolation-by-distance. We observe greater sharing of larger IBD segments between artemisinin-resistant parasites versus sensitive parasites, which is consistent with the recent spread of drug resistance. Our IBD analyses reveal actionable patterns, including isolated parasite populations, which may be prioritized for malaria elimination, as well as asymmetrical migration identifying potential sources and sinks of migrating parasites.
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Affiliation(s)
- Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Graduate Program in Epidemiology and Human Genetics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | | | - Fang Huang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China
| | - Yao Li
- Center for Geospatial Information Science, University of Maryland, College Park, MD, 20742, USA
| | - Sonia Agrawal
- Graduate Program in Epidemiology and Human Genetics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David L Saunders
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Chanthap Lon
- Armed Forces Research Institute of Medical Sciences, Khan Daun Penh, Phnom Penh, Cambodia
| | - Mark M Fukuda
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Pascal Ringwald
- Global Malaria Programme, World Health Organization, Geneva, 1202, Switzerland
| | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Kay Thwe Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, 11191, Myanmar
| | | | - Myaing M Nyunt
- Duke Global Health Institute, Duke University, Durham, NC, 27710, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Kathleen E Stewart
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | | | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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Abstract
The recent Ebola and Zika epidemics demonstrate the need for the continuous surveillance, rapid diagnosis and real-time tracking of emerging infectious diseases. Fast, affordable sequencing of pathogen genomes - now a staple of the public health microbiology laboratory in well-resourced settings - can affect each of these areas. Coupling genomic diagnostics and epidemiology to innovative digital disease detection platforms raises the possibility of an open, global, digital pathogen surveillance system. When informed by a One Health approach, in which human, animal and environmental health are considered together, such a genomics-based system has profound potential to improve public health in settings lacking robust laboratory capacity.
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Affiliation(s)
- Jennifer L. Gardy
- British Columbia Centre for Disease Control, Vancouver, V5Z 4R4 British Columbia Canada
- School of Population and Public Health, University of British Columbia, Vancouver, V6T 1Z3 British Columbia Canada
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT UK
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Abstract
The respiratory tract is a complex organ system that is responsible for the exchange of oxygen and carbon dioxide. The human respiratory tract spans from the nostrils to the lung alveoli and is inhabited by niche-specific communities of bacteria. The microbiota of the respiratory tract probably acts as a gatekeeper that provides resistance to colonization by respiratory pathogens. The respiratory microbiota might also be involved in the maturation and maintenance of homeostasis of respiratory physiology and immunity. The ecological and environmental factors that direct the development of microbial communities in the respiratory tract and how these communities affect respiratory health are the focus of current research. Concurrently, the functions of the microbiome of the upper and lower respiratory tract in the physiology of the human host are being studied in detail. In this Review, we will discuss the epidemiological, biological and functional evidence that support the physiological role of the respiratory microbiota in the maintenance of human health.
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Affiliation(s)
- Wing Ho Man
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA The Netherlands
- Spaarne Gasthuis Academy, Spaarnepoort 1, Hoofddorp, 2134 TM The Netherlands
| | - Wouter A.A. de Steenhuijsen Piters
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA The Netherlands
- The University of Edinburgh/MRC Centre for Inflammation Research, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ UK
| | - Debby Bogaert
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA The Netherlands
- The University of Edinburgh/MRC Centre for Inflammation Research, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ UK
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