1
|
Bager P, Kähler J, Andersson M, Holzknecht BJ, Kjær Hansen SG, Schønning K, Nielsen KL, Koch K, Pinholt M, Voldstedlund M, Larsen AR, Kristensen B, Mølbak K, Sönksen UW, Skovgaard S, Skov R, Hammerum AM. Comparison of morbidity and mortality after bloodstream infection with vancomycin-resistant versus -susceptible Enterococcus faecium: a nationwide cohort study in Denmark, 2010-2019. Emerg Microbes Infect 2024; 13:2309969. [PMID: 38258968 DOI: 10.1080/22221751.2024.2309969] [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: 11/01/2023] [Accepted: 01/19/2024] [Indexed: 01/24/2024]
Abstract
The emergence of bloodstream infections (BSI) caused by vancomycin-resistant Enterococci (VRE) has caused concern. Nonetheless, it remains unclear whether these types are associated with an excess risk of severe outcomes when compared with infections caused by vancomycin-susceptible Enterococci (VSE). This cohort study included hospitalized patients in Denmark with Enterococcus faecium-positive blood cultures collected between 2010 and 2019 identified in the Danish Microbiology Database. We estimated 30-day hazard ratio (HR) of death or discharge among VRE compared to VSE patients adjusted for age, sex, and comorbidity. The cohort included 6071 patients with E. faecium BSI (335 VRE, 5736 VSE) among whom VRE increased (2010-13, 2.6%; 2014-16, 6.3%; 2017-19; 9.4%). Mortality (HR 1.08, 95%CI 0.90-1.29; 126 VRE, 37.6%; 2223 VSE, 37.0%) or discharge (HR 0.89, 95%CI 0.75-1.06; 126 VRE, 37.6%; 2386 VSE, 41.6%) was not different between VRE and VSE except in 2014 (HR 1.87, 95% CI 1.18-2.96). There was no interaction between time from admission to BSI (1-2, 3-14, and >14 days) and HR of death (P = 0.14) or discharge (P = 0.45) after VRE compared to VSE, despite longer time for VRE patients (17 vs. 10 days for VSE, P < 0.0001). In conclusion, VRE BSI was not associated with excess morbidity and mortality. The excess mortality in 2014 only may be attributed to improved diagnostic- and patient-management practices after 2014, reducing time to appropriate antibiotic therapy. The high level of mortality after E. faecium BSI warrants further study.
Collapse
Affiliation(s)
- Peter Bager
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Kähler
- Department of Dataintegration and -Analysis, Statens Serum Institut, Copenhagen, Denmark
| | - Mikael Andersson
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Barbara Juliane Holzknecht
- Department of Clinical Microbiology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Kristian Schønning
- Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Karen Leth Nielsen
- Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Kristoffer Koch
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Marianne Voldstedlund
- Department of Dataintegration and -Analysis, Statens Serum Institut, Copenhagen, Denmark
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- National Reference Laboratory for Antimicrobial Resistance, Statens Serum Institut, Copenhagen, Denmark
| | - Brian Kristensen
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Kåre Mølbak
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health, University of Copenhagen, Denmark
| | - Ute Wolff Sönksen
- National Reference Laboratory for Antimicrobial Resistance, Statens Serum Institut, Copenhagen, Denmark
| | - Sissel Skovgaard
- Department of Clinical Microbiology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
- National Reference Laboratory for Antimicrobial Resistance, Statens Serum Institut, Copenhagen, Denmark
| | - Robert Skov
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anette M Hammerum
- National Reference Laboratory for Antimicrobial Resistance, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
2
|
Huang J, Xiao J, Wang X, Xue X, Ma Y, Zhang Z, Zheng L, Zafir M, Liu P, Zhao X, Larsen AR, Xue H. Unearthing new ccr genes and SCC elements in staphylococci through genome mining. J Infect Dis 2024:jiae044. [PMID: 38271707 DOI: 10.1093/infdis/jiae044] [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: 08/18/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 01/27/2024] Open
Abstract
The SCCmec typing is crucial for investigating methicillin-resistant S. aureus, relying primarily on the combination of ccr and mec gene complexes. To date, 19 ccr genes and 10 ccr gene complexes have been identified, forming 15 SCCmec types. With the vast release of bacterial genome sequences, mining the database for novel ccr gene complexes and SCC/SCCmec elements could enhance MRSA epidemiological studies. In this study, we identified 12 novel ccr genes (6 ccrA, 3 ccrB and 3 ccrC) through mining of the NCBI database, which forming 12 novel ccr gene complexes and 10 novel SCC elements. Overexpression of five groups of novel Ccr recombinases (CcrA9B3, CcrA10B1, CcrC3, CcrC4, and CcrC5) in a mutant MRSA strain lacking the ccr gene and extrachromosomal circular intermediate (ciSCC) production significantly promoted ciSCC production, demonstrating their biological activity. This discovery provides an opportunity to advance MRSA epidemiological research and develop database-based bacterial typing methods.
Collapse
Affiliation(s)
- Jianguo Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jinhe Xiao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xiaokun Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xuemei Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yadong Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Ziqian Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Liangjun Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Muhammad Zafir
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Pilong Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xin Zhao
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Huping Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| |
Collapse
|
3
|
Rinnov MR, Gerner T, Halling AS, Liljendahl MS, Ravn NH, Knudgaard MH, Trautner S, Skov L, Thomsen SF, Egeberg A, Jakasa I, Kezic S, Petersen A, Larsen AR, Dam-Nielsen C, Jarløv JO, Thyssen JP. The association between Staphylococcus aureus colonization on cheek skin at 2 months and subsequent atopic dermatitis in a prospective birth cohort. Br J Dermatol 2023; 189:695-701. [PMID: 37480337 DOI: 10.1093/bjd/ljad249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/31/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
BACKGROUND Staphylococcus aureus may worsen already established atopic dermatitis (AD), but its primary role in the aetiopathogenesis and severity of AD is unclear. OBJECTIVES To compare the prevalence of S. aureus colonization in early infancy in children who developed AD during the first 2 years of life with children who did not. METHODS In this prospective birth cohort study, which included 450 infants, we analysed bacterial swabs collected from cheek skin at 0 and 2 months of age. The development of AD, and its severity, was diagnosed by a physician and monitored prospectively for 2 years. Information on parental atopy, filaggrin gene mutation status and use of antibiotics and emollients was included in the analyses. RESULTS At birth, the occurrence of S. aureus colonization was similar in infants who developed subsequent AD and those who did not. At 2 months of age, S. aureus colonization was more common in children who later developed AD (adjusted hazard ratio 1.97, 95% confidence interval 1.21-3.19; P = 0.006). No association was found between S. aureus colonization and AD severity or age at onset. CONCLUSIONS It remains unknown whether colonization with S. aureus may directly increase the risk of AD, or whether it should be considered as secondary to skin barrier impairment or a skewed immune activity, but according to our findings, S. aureus colonization is more commonly increased at 2 months of age in children who later developed AD.
Collapse
Affiliation(s)
- Maria Rasmussen Rinnov
- Department of Dermatology and Allergy
- Department of Neonatology, Rigshospitalet, University of Copenhagen, Copenhagen Ø, Denmark
| | | | - Anne-Sofie Halling
- Department of Dermatology and Allergy
- Department of Dermatology and Venereology, Bispebjerg Hospital, University of Copenhagen, Bispebjerg Bakke 23, 2400 Copenhagen N, Denmark
| | | | | | | | - Simon Trautner
- Department of Neonatology, Rigshospitalet, University of Copenhagen, Copenhagen Ø, Denmark
| | - Lone Skov
- Department of Dermatology and Allergy
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Simon Francis Thomsen
- Department of Dermatology and Venereology, Bispebjerg Hospital, University of Copenhagen, Bispebjerg Bakke 23, 2400 Copenhagen N, Denmark
| | - Alexander Egeberg
- Department of Dermatology and Venereology, Bispebjerg Hospital, University of Copenhagen, Bispebjerg Bakke 23, 2400 Copenhagen N, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ivone Jakasa
- Laboratory for Analytical Chemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Sanja Kezic
- Amsterdam Public Health Research Institute, Department of Public and Occupational Health Amsterdam UMC, Department of Public and Occupational Health, University of Amsterdam, Amsterdam Public Health Research Institute, 1105 AZ, Amsterdam, the Netherlands
| | - Andreas Petersen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Casper Dam-Nielsen
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Jens Otto Jarløv
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Jacob P Thyssen
- Department of Dermatology and Venereology, Bispebjerg Hospital, University of Copenhagen, Bispebjerg Bakke 23, 2400 Copenhagen N, Denmark
| |
Collapse
|
4
|
Mellergaard M, Skovbakke SL, Jepsen SD, Panagiotopoulou N, Hansen ABR, Tian W, Lund A, Høgh RI, Møller SH, Guérillot R, Hayes AS, Erikstrup LT, Andresen L, Peleg AY, Larsen AR, Stinear TP, Handberg A, Erikstrup C, Howden BP, Goletz S, Frees D, Skov S. Clinical Staphylococcus aureus inhibits human T-cell activity through interaction with the PD-1 receptor. mBio 2023; 14:e0134923. [PMID: 37796131 PMCID: PMC10653905 DOI: 10.1128/mbio.01349-23] [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: 06/07/2023] [Accepted: 08/08/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Therapies that target and aid the host immune defense to repel cancer cells or invading pathogens are rapidly emerging. Antibiotic resistance is among the largest threats to human health globally. Staphylococcus aureus (S. aureus) is the most common bacterial infection, and it poses a challenge to the healthcare system due to its significant ability to develop resistance toward current available therapies. In long-term infections, S. aureus further adapt to avoid clearance by the host immune defense. In this study, we discover a new interaction that allows S. aureus to avoid elimination by the immune system, which likely supports its persistence in the host. Moreover, we find that blocking the specific receptor (PD-1) using antibodies significantly relieves the S. aureus-imposed inhibition. Our findings suggest that therapeutically targeting PD-1 is a possible future strategy for treating certain antibiotic-resistant staphylococcal infections.
Collapse
Affiliation(s)
- Maiken Mellergaard
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Line Skovbakke
- Biotherapeutic Glycoengineering and Immunology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Stine Dam Jepsen
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nafsika Panagiotopoulou
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Amalie Bøge Rud Hansen
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Weihua Tian
- Biotherapeutic Glycoengineering and Immunology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Astrid Lund
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Illum Høgh
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sofie Hedlund Møller
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Romain Guérillot
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ashleigh S. Hayes
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Lars Andresen
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anton Y. Peleg
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Centre to Impact Antimicrobial Resistance, Monash University, Melbourne, Victoria, Australia
| | - Anders Rhod Larsen
- Statens Serum Institute, Microbiology and Infection Control, Copenhagen, Denmark
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Aase Handberg
- Department of Clinical Biochemistry, Aalborg University Hospital, North Denmark Region, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Steffen Goletz
- Biotherapeutic Glycoengineering and Immunology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Dorte Frees
- Food Safety and Zoonosis, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Skov
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
5
|
Ba X, Raisen CL, Restif O, Cavaco LM, Vingsbo Lundberg C, Lee JYH, Howden BP, Bartels MD, Strommenger B, Harrison EM, Larsen AR, Holmes MA, Larsen J. Cryptic susceptibility to penicillin/β-lactamase inhibitor combinations in emerging multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages. Nat Commun 2023; 14:6479. [PMID: 37838722 PMCID: PMC10576800 DOI: 10.1038/s41467-023-42245-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: 04/04/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023] Open
Abstract
Global spread of multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages underscores the need for new therapeutic strategies. Here we show that many S. epidermidis isolates belonging to these lineages display cryptic susceptibility to penicillin/β-lactamase inhibitor combinations under in vitro conditions, despite carrying the methicillin resistance gene mecA. Using a mouse thigh model of S. epidermidis infection, we demonstrate that single-dose treatment with amoxicillin/clavulanic acid significantly reduces methicillin-resistant S. epidermidis loads without leading to detectable resistance development. On the other hand, we also show that methicillin-resistant S. epidermidis is capable of developing increased resistance to amoxicillin/clavulanic acid during long-term in vitro exposure to these drugs. These findings suggest that penicillin/β-lactamase inhibitor combinations could be a promising therapeutic candidate for treatment of a high proportion of methicillin-resistant S. epidermidis infections, although the in vivo risk of resistance development needs to be further addressed before they can be incorporated into clinical trials.
Collapse
Affiliation(s)
- Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Claire L Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Lina Maria Cavaco
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Jean Y H Lee
- Department of Microbiology and 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 Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mette D Bartels
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Birgit Strommenger
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jesper Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark.
| |
Collapse
|
6
|
Tams KW, Larsen I, Hansen JE, Spiegelhauer H, Strøm-Hansen AD, Rasmussen S, Ingham AC, Kalmar L, Kean IRL, Angen Ø, Holmes MA, Pedersen K, Jelsbak L, Folkesson A, Larsen AR, Strube ML. The effects of antibiotic use on the dynamics of the microbiome and resistome in pigs. Anim Microbiome 2023; 5:39. [PMID: 37605221 PMCID: PMC10440943 DOI: 10.1186/s42523-023-00258-4] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/25/2023] [Indexed: 08/23/2023] Open
Abstract
Antibiotics are widely used in pig farming across the world which has led to concerns about the potential impact on human health through the selection of antibiotic resistant pathogenic bacteria. This worry has resulted in the development of a production scheme known as pigs Raised Without Antibiotics (RWA), in which pigs are produced in commercial farms, but are ear-tagged as RWA until slaughter unless they receive treatment, thus allowing the farmer to sell the pigs either as premium priced RWA or as conventional meat. Development of antibiotic resistance in pig farming has been studied in national surveys of antibiotic usage and resistance, as well as in experimental studies of groups of pigs, but not in individual pigs followed longitudinally in a commercial pig farm. In this study, a cohort of RWA designated pigs were sampled at 10 time points from birth until slaughter along with pen-mates treated with antibiotics at the same farm. From these samples, the microbiome, determined using 16S sequencing, and the resistome, as determined using qPCR for 82 resistance genes, was investigated, allowing us to examine the difference between RWA pigs and antibiotic treated pigs. We furthermore included 176 additional pigs from six different RWA farms which were sampled at the slaughterhouse as an endpoint to substantiate the cohort as well as for evaluation of intra-farm variability. The results showed a clear effect of age in both the microbiome and resistome composition from early life up until slaughter. As a function of antibiotic treatment, however, we observed a small but significant divergence between treated and untreated animals in their microbiome composition immediately following treatment, which disappeared before 8 weeks of age. The effect on the resistome was evident and an effect of treatment could still be detected at week 8. In animals sampled at the slaughterhouse, we observed no difference in the microbiome or the resistome as a result of treatment status but did see a strong effect of farm origin. Network analysis of co-occurrence of microbiome and resistome data suggested that some resistance genes may be transferred through mobile genetic elements, so we used Hi-C metagenomics on a subset of samples to investigate this. We conclude that antibiotic treatment has a differential effect on the microbiome vs. the resistome and that although resistance gene load is increased by antibiotic treatment load, this effect disappears before slaughter. More studies are needed to elucidate the optimal way to rear pigs without antibiotics.
Collapse
Affiliation(s)
- Katrine Wegener Tams
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Inge Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1871, Copenhagen, Denmark
| | - Julie Elvekjær Hansen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Henrik Spiegelhauer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | | | - Sophia Rasmussen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300, Copenhagen, Denmark
| | - Lajos Kalmar
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Øystein Angen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300, Copenhagen, Denmark
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Karl Pedersen
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, 751 89, Uppsala, Sweden
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anders Folkesson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300, Copenhagen, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
| |
Collapse
|
7
|
van Soest TM, Søndermølle MB, Brouwer MC, Chekrouni N, Larsen AR, Petersen A, van Sorge NM, Nielsen H, van de Beek D, Bodilsen J. Community-acquired Staphylococcus aureus meningitis in adults. J Infect 2023; 86:239-244. [PMID: 36682629 DOI: 10.1016/j.jinf.2023.01.022] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
BACKGROUND Staphylococcus aureus is an uncommon cause of community-acquired bacterial meningitis. We aimed to describe patients with this disease. METHODS We evaluated clinical characteristics and outcome of adults with community-acquired S. aureus meningitis from prospective nationwide cohort studies from Denmark (2015-2020) and the Netherlands (2006-2021). Whole genome sequencing of S. aureus isolates was performed to evaluate the potential association between clonal complex and clinical characteristics. RESULTS We evaluated 111 episodes of community-acquired S. aureus meningitis: 65 from Denmark and 46 from the Netherlands. The median age was 66 years (interquartile range [IQR] 50-74) and 43 of 111 patients were female (39%). Concomitant infectious foci were found in 95 of 107 patients (89%), most commonly endocarditis (53 of 109 [49%]) and spondylodiscitis (43 of 109 [39%]). The triad of neck stiffness, altered mental status (Glasgow Coma Scale score <14), and fever was present in only 18 of 108 patients (17%). Surgery was performed in 14 of 33 patients (42%) with spondylodiscitis and 26 of 52 (50%) with endocarditis. A favorable outcome (Glasgow Outcome Scale score 5) occurred in 26 of 111 patients (23%), while 39 (35%) died. The most common bacterial clonal complexes (CC) were CC30 (16 [17%]), CC45 (16 [17%]), CC5 (12 [13%], and CC15 (10 [11%]); no associations between CCs and concomitant foci or outcome were found. CONCLUSIONS Community-acquired S. aureus meningitis is a severe disease with a high case fatality rate, occurring mainly in patients with concomitant endocarditis or spondylodiscitis.
Collapse
Affiliation(s)
- Thijs M van Soest
- Department of Neurology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Neurosciences, Neuroinfection and - Inflammation, Amsterdam, the Netherlands; European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland
| | - Maria Birgitte Søndermølle
- European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland; Department of Infectious Diseases, Aalborg University Hospital, Mølleparkvej 4, Aalborg 9000, Denmark
| | - Matthijs C Brouwer
- Department of Neurology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Neurosciences, Neuroinfection and - Inflammation, Amsterdam, the Netherlands; European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland
| | - Nora Chekrouni
- Department of Neurology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Neurosciences, Neuroinfection and - Inflammation, Amsterdam, the Netherlands; European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland
| | | | | | - Nina M van Sorge
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
| | - Henrik Nielsen
- European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland; Department of Infectious Diseases, Aalborg University Hospital, Mølleparkvej 4, Aalborg 9000, Denmark
| | - Diederik van de Beek
- Department of Neurology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Neurosciences, Neuroinfection and - Inflammation, Amsterdam, the Netherlands; European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland
| | - Jacob Bodilsen
- European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland; Department of Infectious Diseases, Aalborg University Hospital, Mølleparkvej 4, Aalborg 9000, Denmark.
| | | |
Collapse
|
8
|
Frimodt-Møller N, Simonsen GS, Larsen AR, Kahlmeter G. Pivmecillinam, the paradigm of an antibiotic with low resistance rates in Escherichia coli urine isolates despite high consumption. J Antimicrob Chemother 2022; 78:289-295. [PMID: 36441168 DOI: 10.1093/jac/dkac396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/22/2022] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Pivmecillinam, the oral version of mecillinam, represents one of the major recommended and used antibiotics for empiric and targeted treatment of urinary tract infections in primary care in Denmark, Norway and Sweden. Mecillinam resistant mutants in Escherichia coli develop easily in vitro, but their fitness cost has been shown to be high. METHODS We revisited the resistance and consumption data from the monitoring programmes in the three countries and compared pivmecillinam with ciprofloxacin from 2010 to 2020. RESULTS Mecillinam resistance rates in Escherichia coli remained around 6% in Denmark and Norway relative to a constant consumption in Norway of 1.6-1.8 DID (defined daily doses per 1000 inhabitants per day), and even increasing in Denmark from 1.6 to 2.3 DID. In Sweden resistance was significantly lower at 4% related to the lower consumption of 0.5 DID. For ciprofloxacin, resistance rates fluctuated around 6%-12%, highest in Sweden with the highest consumption (0.8-0.6 DID) and lowest in Denmark (0.55-0.35 DID) and Norway (0.7-0.3 DID), although consumption declined significantly in all three countries. CONCLUSIONS Pivmecillinam is an example of an antibiotic, which easily develops resistance in vitro, but apparently can be used broadly in primary care without increase in resistance rates.
Collapse
Affiliation(s)
- Niels Frimodt-Møller
- Department of Clinical Microbiology, Rigshospitalet, DK2100, Copenhagen, Denmark
| | - Gunnar Skov Simonsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, and Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Gunnar Kahlmeter
- Department of Clinical Microbiology, Central Hospital, Växjö, Sweden
| |
Collapse
|
9
|
Coppens J, Xavier BB, Vlaeminck J, Larsen J, Lammens C, Van Puyvelde S, Goossens H, Larsen AR, Malhotra-Kumar S. Genomic analysis of methicillin-resistant Staphylococcus aureus clonal complex 239 isolated from Danish patients with and without an international travel history. Front Microbiol 2022; 13:1016829. [PMID: 36504833 PMCID: PMC9730231 DOI: 10.3389/fmicb.2022.1016829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 08/11/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction International travel has been a major determinant for the introduction of pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) into naïve geographic areas. MRSA clonal complex 239 (CC239) is a highly virulent clone that is predominant in Asia. The objective of this study was to determine the geographic origin of MRSA CC239 isolates recovered from Danish cases with or without a history of international travel during 2004-2016. Materials and methods Human MRSA isolates with spa types t030 and t037 (n = 60) were obtained from the National Reference Laboratory for Antimicrobial Resistance. For each case, the following data were collected from notification forms: sex, age, isolation year, specimen source (screening swab or clinical sample), infection type, and international travel history. All isolates were whole-genome sequenced, and a comparative genome and phylogenetic analysis was performed. Results The majority of isolates originated from skin and soft tissue (SST) infections and screening swabs. In 31 out of 60 cases reported international travel to different parts of the world. Fifty-four isolates belonged to CC239, including sequence type 239 (ST239) (n = 43), ST241 (n = 5), ST4377 (n = 2), ST4378 (n = 1), ST1465 (n = 1), ST343 (n = 1), and ST592 (n = 1). The majority of the CC239 MRSA isolates (40/54) belonged to well-known geographic clades, including the Asian (n = 12), Serbian (n = 11), South American (n = 2), and Turkish (n = 15). Most MRSA ST239 isolates belonging to the highly virulent Asian clade carried sasX and were recovered from individuals who had travelled to Asia, Africa and the Middle East. Conclusion Our data reveal multiple introductions of MRSA CC239 into Denmark through international travel, which highlights the importance of continued genomic surveillance of MRSA in persons returning from international travel to areas where MRSA is endemic.
Collapse
Affiliation(s)
- Jasmine Coppens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Jelle Vlaeminck
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Sandra Van Puyvelde
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium,Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium,*Correspondence: Surbhi Malhotra-Kumar,
| |
Collapse
|
10
|
Bengtsen K, Fosboel E, Haugan K, Philbert BT, Johansen JB, Torp-Pedersen C, Riahi S, Nielsen JC, Petersen A, Larsen AR, Bruun NE, Ruwald AC. Staphylococcus aureus bacteremia in Danish patients with cardiac implantable electronic devices: an explorative epidemiological study. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.1677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Device-related infection is the most common serious complication in patients with cardiac implantable electronic devices (CIED). Staphylococcus aureus accounts for up to 30% of CIED-related infections. There is a lack of scientific literature investigating risk of Staphylococcus aureus bacteremia (SAB) in CIED-patients.
Purpose
We aimed to describe the risk of SAB in Danish patients with a CIED through the years 2000–2018 compared to the background population.
Methods
Patients who received a CIED from 2000–2018 were identified from The Danish National Pacemaker and ICD Register. Patients were matched 1:5 on age and gender with the background population. We identified the primary endpoint of first time SAB from The National Danish Staphylococcus Aureus Bacteremia Database. The cumulative incidence of SAB was calculated using the Aalen-Johansen estimator, adding competing risk of death into account. Hazard ratios were estimated by Cox regression models adjusting for age and gender. Crude rates of relapse SAB, defined as a new SAB episode 14–180 days after first SAB, and device extractions were reported for all patients who survived 14 days from SAB diagnosis.
Results
We identified 79,324 CIED-patients (pacemaker (PM) = 61,227; Implantable Cardioverter Defibrillator (ICD) = 11,635; Cardiac resynchronization therapy, PM or ICD (CRT) = 6,364 and 396,590 matched controls (median age 75.5±13.3 years; 61% males). Age and gender distribution differed significantly by device type (age: PM 76.1±12.1; ICD 62.4±13.4; CRT 68.0±11.1; males: PM: 55.6%, ICD% 75.5: CRT: 80.9%). Across a mean follow-up of 5.9 (±4.6) years, we observed first episode of SAB in 1,430 (1.8%) CIED-patients, compared to 2,599 (0.7%) patients in the control population (p<0.001).
The 10-year cumulative incidence of SAB was 1.0% for controls and 2.2% for CIED patients. The risk of SAB differed substantially by device type (Figure 1). Compared to controls and adjusted for age and gender, increasing hazard ratios for SAB were observed with more advanced devices: PM 1.12 (1.11–1.13); ICD 1.36 (1.33–1.39); CRT 1.55 (1.51–1.59). However, CIED-patients with SAB did not have higher 30-day mortality rates than the non-CIED control population with SAB (Controls 34.8%; PM 35.1%; ICD 28.1% CRT 26.1%, p=0.016). Out of all SAB patients who survived 14 days from SAB diagnosis (Controls=1,672; CIED=1,107), relapse SAB occurred in 52 (3.1%) controls and in 51 (4.6%) CIED-patients (PM 4.0%; ICD 5.8%; CRT 6.3%). Device extraction within 14 and 30 days from SAB diagnosis was undertaken in less than 30% of the CIED-patients (PM: 11.3/13.6%; ICD: 22.7/27.5%; CRT: 17.4/20.1%).
Conclusion
The occurrence of SAB was higher in CIED patients compared with controls and increased with more advanced devices. There was no difference in 30-day mortality after SAB between CIED patients and controls. Relapse SAB occurred in less than 7%, despite a low percentage of early device extractions.
Funding Acknowledgement
Type of funding sources: None.
Collapse
Affiliation(s)
- K Bengtsen
- Zealand University Hospital , Roskilde , Denmark
| | - E Fosboel
- Rigshospitalet - Copenhagen University Hospital , Copenhagen , Denmark
| | - K Haugan
- Zealand University Hospital , Roskilde , Denmark
| | - B T Philbert
- Rigshospitalet - Copenhagen University Hospital , Copenhagen , Denmark
| | | | | | - S Riahi
- Aalborg University Hospital , Aalborg , Denmark
| | - J C Nielsen
- Aarhus University Hospital , Aarhus , Denmark
| | - A Petersen
- Statens Serum Institut , Copenhagen , Denmark
| | - A R Larsen
- Statens Serum Institut , Copenhagen , Denmark
| | - N E Bruun
- Zealand University Hospital , Roskilde , Denmark
| | - A C Ruwald
- Zealand University Hospital , Roskilde , Denmark
| |
Collapse
|
11
|
Rakonjac B, Lepšanović Z, Šuljagić V, Jovčić B, Kojić M, Larsen AR, Đurić M, Ćirković I. Predominance of t355/ST152/SCCmec V clonal type among PVL-positive MRSA isolates in a tertiary care hospital in Belgrade, Serbia. PLoS One 2022; 17:e0273474. [PMID: 36074767 PMCID: PMC9455871 DOI: 10.1371/journal.pone.0273474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/09/2022] [Indexed: 11/19/2022] Open
Abstract
Epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) is continually changing. Frequency of genotypes typical for community-associated MRSA (CA-MRSA) is increasing in hospitals, as well as resistance to antimicrobial agents. Moreover, different clones predominate in different geographic regions, and temporal shifts occur in the predominant clonal type. The aim of this study was to estimate the prevalence of MRSA, CA-MRSA and PVL-positive MRSA isolates from patients hospitalised in the Military Medical Academy (MMA) and from outpatients, and to perform genotyping of PVL-positive MRSA isolates. MRSA isolates were obtained by standard microbiological techniques. PVL-positive MRSA were detected by single PCR. Determination of SCCmec types in MRSA isolates was done using multiplex PCR and genotyping of PVL-positive MRSA by PFGE, MLST and spa typing. The prevalence of MRSA among S. aureus isolates from different clinical specimens was 43.4%. In outpatients the prevalence of MRSA was 3.2%. SCCmec types specific for CA-MRSA were found in 26% of MRSA isolates from hospitalised patients. In groups, hospitalised patients and outpatients, the prevalence of PVL-positive MRSA isolates was 4%, and all of them harboured SCCmec type V genetic element. PFGE revealed minor differences between four groups of PVL-positive MRSA isolates, but all of them belonged to ST152, and all except one were of the t355 spa type. High prevalence of MRSA and CA-MRSA in MMA, especially the presence of PVL-positive CA-MRSA, represent a serious health threat for patients. Genotype t355/ST152/SCCmec V is the dominant MRSA clone among PVL-positive CA-MRSA.
Collapse
Affiliation(s)
| | - Zorica Lepšanović
- Military Medical Academy, Belgrade, Serbia
- Medical Faculty, University of Defence, Belgrade, Serbia
| | - Vesna Šuljagić
- Military Medical Academy, Belgrade, Serbia
- Medical Faculty, University of Defence, Belgrade, Serbia
| | - Branko Jovčić
- Institute of Molecular Genetics and Genetic Engineering, Univerity of Belgrade, Belgrade, Serbia
| | - Milan Kojić
- Institute of Molecular Genetics and Genetic Engineering, Univerity of Belgrade, Belgrade, Serbia
| | - Anders Rhod Larsen
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Ivana Ćirković
- University of Belgrade-Faculty of Medicine, Institute of Microbiology and Immunology, Belgrade, Serbia
- * E-mail:
| |
Collapse
|
12
|
Nielsen RT, Dalby T, Emborg HD, Larsen AR, Petersen A, Torpdahl M, Hoffmann S, Vestergaard LS, Valentiner-Branth P. COVID-19 preventive measures coincided with a marked decline in other infectious diseases in Denmark, spring 2020. Epidemiol Infect 2022; 150:e138. [PMID: 35899864 PMCID: PMC9343452 DOI: 10.1017/s0950268822001145] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We aimed to descriptively analyse the possible impact of the national COVID-19 interventions on the incidence of common infectious diseases in Denmark during spring and summer 2020. This observational study focused on national register data on infections caused by 16 different bacterial and viral pathogens. We included new cases registered between 1 January 2016 and 31 July 2020. The weekly number of new cases were analysed with respect to the COVID-19-related interventions introduced during 2020. We found a marked decrease in infections associated with droplet transmission coinciding with the COVID-19 interventions in spring and summer 2020. These included decreases in both viral and bacterial airway infections and also decreases in invasive infections caused by Streptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis. There was also a reduction in cases associated with foodborne transmission during the COVID-19 lockdown period. We found no effect of the lockdown on infections by invasive beta-haemolytic streptococci group B, C and G, Staphylococcus aureus bacteraemia, Neisseria gonorrhoeae or Clostridioides difficile. In conclusion, we found that the widespread interventions such as physical distancing, less travel, hygiene measures and lockdown of schools, restaurants and workplaces together coincided with a marked decline in respiratory infections and, to a smaller extent, some foodborne-transmitted infections.
Collapse
Affiliation(s)
- Rikke Thoft Nielsen
- Department of Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Tine Dalby
- Department of Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
- Author for correspondence: Tine Dalby, E-mail:
| | - Hanne-Dorthe Emborg
- Department of Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Andreas Petersen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mia Torpdahl
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Steen Hoffmann
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Lasse Skafte Vestergaard
- Department of Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Palle Valentiner-Branth
- Department of Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
13
|
Baede VO, David MZ, Andrasevic AT, Blanc DS, Borg M, Brennan G, Catry B, Chabaud A, Empel J, Enger H, Hallin M, Ivanova M, Kronenberg A, Kuntaman K, Larsen AR, Latour K, Lindsay JA, Pichon B, Santosaningsih D, Schouls LM, Vandenesch F, Werner G, Żabicka D, Žemličková H, Seifert H, Vos MC. MRSA surveillance programmes worldwide: moving towards a harmonised international approach. Int J Antimicrob Agents 2022; 59:106538. [PMID: 35091055 DOI: 10.1016/j.ijantimicag.2022.106538] [Citation(s) in RCA: 2] [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: 07/23/2021] [Revised: 12/15/2021] [Accepted: 01/19/2022] [Indexed: 11/23/2022]
Abstract
Multinational surveillance programmes for methicillin-resistant Staphylococcus aureus (MRSA) are dependent on national structures for data collection. This study aimed to capture the diversity of national MRSA surveillance programmes and to propose a framework for harmonisation of MRSA surveillance. The International Society of Antimicrobial Chemotherapy (ISAC) MRSA Working Group conducted a structured survey on MRSA surveillance programmes and organised a webinar to discuss the programmes' strengths and challenges as well as guidelines for harmonisation. Completed surveys represented 24 MRSA surveillance programmes in 16 countries. Several countries reported separate epidemiological and microbiological surveillance. Informing clinicians and national policy-makers were the most common purposes of surveillance. Surveillance of bloodstream infections (BSIs) was present in all programmes. Other invasive infections were often included. Three countries reported active surveillance of MRSA carriage. Methodology and reporting of antimicrobial susceptibility, virulence factors, molecular genotyping and epidemiological metadata varied greatly. Current MRSA surveillance programmes rely upon heterogeneous data collection systems, which hampers international epidemiological monitoring and research. To harmonise MRSA surveillance, we suggest improving the integration of microbiological and epidemiological data, implementation of central biobanks for MRSA isolate collection, and inclusion of a representative sample of skin and soft-tissue infection cases in addition to all BSI cases.
Collapse
Affiliation(s)
- Valérie O Baede
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Michael Z David
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arjana Tambic Andrasevic
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, University of Zagreb School of Dental Medicine, Zagreb, Croatia
| | - Dominique S Blanc
- Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance, Lausanne site, Lausanne, Switzerland
| | - Michael Borg
- Department of Infection Control, Mater Dei Hospital, Msida, Malta
| | - Grainne Brennan
- National MRSA Reference Laboratory, St James's Hospital, Dublin 8, Ireland
| | - Boudewijn Catry
- Healthcare-associated infections & antimicrobial resistance, Sciensano, Brussels, Belgium; Faculty of Medicine, Université libre de Bruxelles, Brussels, Belgium
| | - Aurélie Chabaud
- Mission nationale SPARES (Surveillance et Prévention de l'AntibioRésistance en Etablissement de santé), Limoges University Hospital, Limoges, France
| | - Joanna Empel
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Hege Enger
- The Norwegian MRSA Reference Laboratory, St Olavs Hospital, Trondheim, Norway
| | - Marie Hallin
- Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Marina Ivanova
- East-Tallinn Central Hospital Laboratory, Tallinn, Estonia
| | - Andreas Kronenberg
- Swiss Centre for Antibiotic Resistance, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Kuntaman Kuntaman
- Department of Medical Microbiology, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia; Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Anders Rhod Larsen
- National Reference Laboratory for Antimicrobial Resistance, Department of Bacteria, Fungi and Parasites, Statens Serum Institut, Copenhagen, Denmark
| | - Katrien Latour
- Healthcare-associated infections & antimicrobial resistance, Sciensano, Brussels, Belgium
| | - Jodi A Lindsay
- Institute for Infection and Immunity, St George's, University of London, London, UK
| | - Bruno Pichon
- National Infection Service, Public Health England, London, UK
| | - Dewi Santosaningsih
- Department of Clinical Microbiology, Faculty of Medicine, Brawijaya University/Dr Saiful Anwar Hospital, Malang, Indonesia
| | - Leo M Schouls
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - François Vandenesch
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Guido Werner
- Robert Koch Institute, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, Germany
| | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Helena Žemličková
- National Reference Laboratory for Antibiotics, Centre for Epidemiology and Microbiology, National Institute of Public Health, 10000 Prague, Czech Republic; Department of Microbiology, 3rd Faculty of Medicine Charles University, University Hospital Kralovske Vinohrady and National Institute of Public Health, 10000 Prague, Czech Republic
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Köln, Germany
| | - Margreet C Vos
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
| |
Collapse
|
14
|
Larsen AR, Henriksen AS, Frimodt-Møller N. 1428. Increased Consumption of Pivmecillinam in Primary Care for Uncomplicated Urinary Tract Infection (uUTI) Is Not Associated With Increased Resistance Rates. Open Forum Infect Dis 2021. [PMCID: PMC8644580 DOI: 10.1093/ofid/ofab466.1620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background The evolution of antibiotic resistance in Escherichia coli (E. coli) hampers the treatment of UTIs, mirroring the global public health concerns around antimicrobial resistance. Pivmecillinam, an oral prodrug of mecillinam (a β-lactam antibiotic), is used as first-line treatment for uUTIs in Denmark. Here, we examine the use of, and the prevalence of resistance to, mecillinam in Denmark in the primary care setting. Methods Nationwide data on the use of and resistance to pivmecillinam (reported as its active form, mecillinam) was extracted and examined from the Danish Integrated Antimicrobial Resistance Monitoring and Research Programme (DANMAP) 2019 report (www.danmap.org). Prevalence estimates of resistance reported by DANMAP 2019 were obtained from the Danish Microbiology Database (MiBA). Results In 2019, pivmecillinam accounted for about 27% of penicillins and 75% of penicillins with extended spectrum consumed in primary healthcare in Denmark. Pivmecillinam usage has increased primarily due to changes in recommendations for the treatment of uUTIs. Between 2010 and 2019, pivmecillinam usage in Denmark increased by 45% from 1.67 to 2.43, defined as daily doses per 1,000 inhabitants per day. In 2019, analysis of 83,850 urinary isolates from patients in the primary care setting with E. coli revealed a 5.3% resistance rate to mecillinam. Time-trend analysis using data from a 10-year period showed a small but significant decrease from the 5.5% resistance rate recorded in 2010 (p=0.001). In general, in spite of increasing use in Denmark, the development of resistance to pivmecillinam has remained low. In fact, a slight decline in pivmecillinam resistance was observed over the past decade. Conclusion Despite the rising number of UTIs and the increasing use of pivmecillinam for uUTI in Denmark, over the past decade, the development of resistance to pivmecillinam remains low. Disclosures Anne Santerre Henriksen, MS, Advanz (Consultant)Shionogi BV (Consultant)UTILITY Therapeutics (Consultant)
Collapse
|
15
|
Kaur KP, Chaudry MS, Chamat-Hedemand S, Larsen AR, Pedersen A, Fosboel EL, Oestergaard L, Torp-Pedersen C, Bruun NE. Risk of infective endocarditis in patients with Staphylococcus aureus blood stream infection and declining kidney function. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.2923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Worldwide, Staphylococcus aureus (S.aureus) is one the most common causes of infective endocarditis (IE), particularly in dialysis patients. However, the association between mildly and moderately decreased kidney function and IE in patients with S.aureus blood stream infection (SAB) has not been examined.
Purpose
In a retrospective nation-wide study, to evaluate the association between IE and declining kidney function in SAB patients.
Methods
All patients with first-time SAB between January 1st, 1996 to December 31st, 2018 were identified from a national database including >90% of all patients with SAB. By cross-linking with other nationwide databases, co-morbidities were recorded. The population was divided into 4 groups according to eGFR: group 1 (eGFR ≥90), group 2 (eGFR 30–89), group 3 (eGFR <30) and group 4 (Renal Replacement Therapy dependent). Patients were followed until the outcome of IE. Changes in co-morbidities across the eGFR groups were tested with the Cochran-Armitage test. In a multivariable logistic regression analysis, the odds ratio (OR) of IE was calculated for each eGFR group while adjusting for age, sex, hypertension, diabetes, native valve disease (NVD), prosthetic valve, and cardiac implantable electronic device (CIED).
Results
Among 17,759 SAB patients, 1,098 were diagnosed with IE. The male population accounted for 60–70% of the IE patients in each eGFR group (Table 1). The overall median age of S.aureus IE patients was 61.5 [48–72] with the highest median age in group 2 (67 [57–76]). Across the eGFR groups, there was a significant increase in the prevalence of diabetes (12.6% in group 1 to 47.0% in group 4), hypertension (18.9% in group 1 to 80% in group 4) and native valve disease (18.7% in group 1 to 36.4% in group 4), p<0.0001. In a multivariate analysis with group 1 as reference, the adjusted OR of S.aureus IE increased significantly with OR 1.16 [95% CI 1.01–1.34] in group 2 to OR 1.42 [95% CI 1.07–1.87] in group 3. The increase was not significant in group 4, OR 1.63 [95% CI 0.95–2.53]. The OR of S.aureus IE decreased with increasing age groups and OR was 0.55 [95% CI 0.43–0.71] among patients >80 years as compared to the reference age group, 18–39 years. A significantly increased OR of S.aureus IE was found among patients with NVD (OR 3.25 [95% CI 2.22–4.76]), prosthetic valve (OR 6.31 [95% CI 5.10–7.79] and CIED (OR 2.88 [95% CI 2.35–3.53]). The overall in-hospital mortality was 16.4% (n=181), with the highest mortality in group 3 (n=11, 22.3%). Overall, the one-year mortality was 26.6% (n=292), and the highest mortality was found in group 4 (n=29, 34.1%). When adjusting for age and sex, mortality did not differ significantly with declining eGFR.
Conclusion
In this study, we found a significant increase in the odds ratio of IE in patients with SAB when kidney function decreased. Both in-hospital and one-year mortality were high, but did not differ significantly across the eGFR groups.
Funding Acknowledgement
Type of funding sources: None.
Collapse
Affiliation(s)
- K P Kaur
- Zealand University Hospital, Department of Cardiology, Roskilde, Denmark
| | - M S Chaudry
- Herlev and Gentofte Hospital, Department of Cardiology, Copenhagen, Denmark
| | - S Chamat-Hedemand
- Zealand University Hospital, Department of Cardiology, Roskilde, Denmark
| | - A R Larsen
- Statens Serum Institut, Copenhagen, Denmark
| | - A Pedersen
- Statens Serum Institut, Copenhagen, Denmark
| | - E L Fosboel
- Rigshospitalet - Copenhagen University Hospital, The Heart Center, Copenhagen, Denmark
| | - L Oestergaard
- Rigshospitalet - Copenhagen University Hospital, The Heart Center, Copenhagen, Denmark
| | - C Torp-Pedersen
- Aalborg University Hospital, Department of Cardiology and Clinical Epidemiology, Aalborg, Denmark
| | - N E Bruun
- Zealand University Hospital, Department of Cardiology, Roskilde, Denmark
| |
Collapse
|
16
|
Widerström M, Stegger M, Johansson A, Gurram BK, Larsen AR, Wallinder L, Edebro H, Monsen T. Heterogeneity of Staphylococcus epidermidis in prosthetic joint infections: time to reevaluate microbiological criteria? Eur J Clin Microbiol Infect Dis 2021; 41:87-97. [PMID: 34599708 PMCID: PMC8732909 DOI: 10.1007/s10096-021-04352-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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/17/2021] [Indexed: 11/24/2022]
Abstract
Prosthetic joint infection (PJI) is a feared and challenging to diagnose complication after arthroplasty, with Staphylococcus epidermidis as the major pathogen. One important criteria to define PJI is the detection of phenotypically indistinguishable microorganisms with identical antibiotic susceptibility pattern in at least two different samples. However, owing to phenotypical variation within genetic clones and clonal variation within a phenotype, the criteria may be ambiguous. We investigated the extent of diversity among coagulase-negative staphylococci (CoNS) in PJI and characterised S. epidermidis isolates from PJI samples, specifically multiple S. epidermidis isolates identified in individual PJI patients. We performed a retrospective cohort study on 62 consecutive patients with PJI caused by CoNS from two hospitals in Northern Sweden. In 16/62 (26%) PJIs, multiple S. epidermidis isolates were available for whole-genome analyses. Hospital-adapted multidrug-resistant genetic clones of S. epidermidis were identified in samples from 40/62 (65%) of the patients using a combination of pulsed-field gel electrophoresis and multilocus sequence typing. Whole-genome sequencing showed the presence of multiple sequence types (STs) in 7/16 (44%) PJIs where multiple S. epidermidis isolates were available. Within-patient phenotypical variation in the antibiotic susceptibility and/or whole-genome antibiotic resistance gene content was frequent (11/16, 69%) among isolates with the same ST. The results highlight the ambiguity of S. epidermidis phenotypic characterisation as a diagnostic method in PJI and call for larger systematic studies for determining the frequency of CoNS diversity in PJIs, the implications of such diversity for microbiological diagnostics, and the therapeutic outcomes in patients.
Collapse
Affiliation(s)
- Micael Widerström
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden.
| | - Marc Stegger
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Johansson
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
| | - Bharat Kumar Gurram
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Lars Wallinder
- Department of Orthopaedics, University Hospital of Umeå, Umeå, Sweden
| | - Helen Edebro
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
| | - Tor Monsen
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
| |
Collapse
|
17
|
Eriksen HB, Petersen A, Pedersen M, Overballe-Petersen S, Larsen AR, Holzknecht BJ. Possible misinterpretation of penicillin susceptibility in Staphylococcus aureus blood isolate due to in vitro loss of the blaZ gene. Eur J Clin Microbiol Infect Dis 2021; 41:163-167. [PMID: 34529167 DOI: 10.1007/s10096-021-04344-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/06/2021] [Indexed: 10/20/2022]
Abstract
We describe a case of recurrent catheter-related blood stream infections (BSI) with Staphylococcus aureus, in which the first isolate tested susceptible to penicillin, while subsequent isolates were resistant. Phenotypic susceptibility correlated with the absence/presence of the blaZ gene. The in vitro stability of penicillin resistance was investigated by subculturing single colonies. In two out of five colonies, phenotypical resistance was lost after a single subculture, which correlated with loss of the blaZ gene. This in vitro phenomenon probably resulted in a very major error in the microbiology report of the first BSI, where penicillin had been recommended as treatment.
Collapse
Affiliation(s)
- Helle Brander Eriksen
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte, Borgmester Ib Juuls Vej 52, 5., 2730, Copenhagen, Herlev, Denmark.
| | - Andreas Petersen
- National Reference Laboratory for Antimicrobial Resistance, Statens Serum Institut, Copenhagen, Denmark
| | - Michael Pedersen
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Søren Overballe-Petersen
- National Reference Laboratory for Antimicrobial Resistance, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- National Reference Laboratory for Antimicrobial Resistance, Statens Serum Institut, Copenhagen, Denmark
| | - Barbara Juliane Holzknecht
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte, Borgmester Ib Juuls Vej 52, 5., 2730, Copenhagen, Herlev, Denmark
| |
Collapse
|
18
|
Angen Ø, Nielsen MW, Løfstrøm P, Larsen AR, Hendriksen NB. Airborne Spread of Methicillin Resistant Staphylococcus aureus From a Swine Farm. Front Vet Sci 2021; 8:644729. [PMID: 34150881 PMCID: PMC8211894 DOI: 10.3389/fvets.2021.644729] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Spread of livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) to farmworkers has been recognized as a risk when working in LA-MRSA positive stables, due to LA-MRSA being present on airborne dust particles. Based on this, airborne spread of LA-MRSA through stable vents is a concern that is addressed in this study. The aim of the investigation was to quantify the airborne spread of LA-MRSA from a MRSA positive swine farm. In order to achieve this, a method for sampling large volumes of air was applied. The results were compared to meteorological data and bacteriological investigation of samples from the air inside the swine barn, soil outside the farm, and nasal samples from the individuals participating in the sampling process. MRSA was detected up to 300 m (the maximal measuring distance) from the swine farm in the air but only at low levels at distances above 50 meters (0.085 CFU/m3 at a distance of 50 m in the wind plume). MRSA was detected in sock samples obtained at the soil surfaces up to 400 m (the maximal measuring distance) from the farm building. The proportion of MRSA positive soil samples decreased from ~80 to 30% with increasing distance from the farm. A total of 25 human nasal samples were sampled after the farm visits after the participants had stayed in the surroundings of the farm for an average of 10.5 h. When leaving the farm, only two of the samples (8%) were LA-MRSA-positive both obtained from one individual who was the one who had sampled the ventilation shafts. In conclusion, airborne spread of MRSA from swine farms does not seem to be an important route for human contamination for individuals staying a whole working day outside a swine farm.
Collapse
Affiliation(s)
- Øystein Angen
- Department of Bacteriology, Parasitology, and Mycology, Statens Serum Institut, Copenhagen, Denmark
| | - Martin Weiss Nielsen
- Department of Microbiology and Production, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Per Løfstrøm
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Anders Rhod Larsen
- Department of Bacteriology, Parasitology, and Mycology, Statens Serum Institut, Copenhagen, Denmark
| | | |
Collapse
|
19
|
Skov R, Lonsway DR, Larsen J, Larsen AR, Samulioniené J, Limbago BM. Evaluation of methods for detection of β-lactamase production in MSSA. J Antimicrob Chemother 2021; 76:1487-1494. [PMID: 33615356 DOI: 10.1093/jac/dkab032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/08/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Correct determination of penicillin susceptibility is pivotal for using penicillin in the treatment of Staphylococcus aureus infections. This study examines the performance of MIC determination, disc diffusion and a range of confirmatory tests for detection of penicillin susceptibility in S. aureus. METHODS A total of 286 consecutive penicillin-susceptible S. aureus blood culture isolates as well as a challenge set of 62 MSSA isolates were investigated for the presence of the blaZ gene by PCR and subjected to penicillin-susceptibility testing using broth microdilution MIC determination, disc diffusion including reading of the zone edge, two nitrocefin tests and the cloverleaf test. RESULTS Using PCR-based detection of blaZ as the gold standard, both broth microdilution MIC testing and disc diffusion testing resulted in a relatively low accuracy (82%-93%) with a sensitivity ranging from 49%-93%. Among the confirmatory tests, the cloverleaf test performed with 100% accuracy, while zone edge interpretation and nitrocefin-based tests increased the sensitivity of β-lactamase detection to 96%-98% and 82%-96% when using MIC determination or disc diffusion as primary test, respectively. CONCLUSIONS This investigation showed that reliable and accurate detection of β-lactamase production in S. aureus can be obtained by MIC determination or penicillin disc diffusion followed by interpretation of the zone edge as a confirmatory test for apparently penicillin-susceptible isolates. The more cumbersome cloverleaf test can also be used. Nitrocefin-based tests should not be used as the only test for confirmation of a presumptive β-lactamase-negative isolate.
Collapse
Affiliation(s)
- Robert Skov
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - David R Lonsway
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jesper Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jurgita Samulioniené
- Department of Clinical Microbiology, Aalborg University Hospital, Alborg, Denmark
| | - Brandi M Limbago
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|
20
|
Egyir B, Bentum J, Attram N, Fox A, Obeng-Nkrumah N, Appiah-Korang L, Behene E, Kumordjie S, Yeboah C, Agbodzi B, Bentil RE, Tagoe R, Kofi Adu Tabi B, Owusu F, Dayie NTKD, Donkor ES, Nsaful J, Asah-Opoku K, Nyarko E, Asumanu E, Larsen AR, Wolfe DM, Letizia AG. Whole Genome Sequencing and Antimicrobial Resistance of Staphylococcus aureus from Surgical Site Infections in Ghana. Pathogens 2021; 10:pathogens10020196. [PMID: 33673230 PMCID: PMC7918159 DOI: 10.3390/pathogens10020196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 01/20/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is a common cause of surgical site infections (SSIs) globally. Data on the occurrence of methicillin-susceptible S. aureus (MSSA) as well as methicillin-resistant S. aureus (MRSA) among patients with surgical site infections (SSIs) in sub-Saharan African are scarce. We characterized S. aureus from SSIs in Ghana using molecular methods and antimicrobial susceptibility testing (AST). Wound swabs or aspirate samples were collected from subjects with SSIs. S. aureus was identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF-MS); AST was performed by Kirby-Bauer disk diffusion, and results were interpreted according to the Clinical and Laboratory Standards Institute (CLSI) guideline. Detection of spa, mecA, and pvl genes was performed by polymerase chain reaction (PCR). Whole-genome sequencing (WGS) was done using the Illumina MiSeq platform. Samples were collected from 112 subjects, with 13 S. aureus isolates recovered. Of these, 92% were sensitive to co-trimoxazole, 77% to clindamycin, and 54% to erythromycin. Multi-drug resistance was detected in 5 (38%) isolates. The four mecA gene-positive MRSA isolates detected belonged to ST152 (n = 3) and ST5 (n = 1). In total, 62% of the isolates were positive for the Panton-Valentine leukocidin (pvl) toxin gene. This study reports, for the first time, a pvl-positive ST152-t355 MRSA clone from SSIs in Ghana. The occurrence of multi-drug-resistant S. aureus epidemic clones suggests that continuous surveillance is required to monitor the spread and resistance trends of S. aureus in hospital settings in the country.
Collapse
Affiliation(s)
- Beverly Egyir
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra 00233, Ghana; (J.B.); (R.T.); (B.K.A.T.); (F.O.)
- Correspondence:
| | - Jeannette Bentum
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra 00233, Ghana; (J.B.); (R.T.); (B.K.A.T.); (F.O.)
- Naval Medical Research Unit—Three, Ghana Detachment, Accra 00233, Ghana; (N.A.); Ghana; (A.F.); (E.B.); (S.K.); (C.Y.); (B.A.); (R.E.B.); (D.M.W.); (A.G.L.)
| | - Naiki Attram
- Naval Medical Research Unit—Three, Ghana Detachment, Accra 00233, Ghana; (N.A.); Ghana; (A.F.); (E.B.); (S.K.); (C.Y.); (B.A.); (R.E.B.); (D.M.W.); (A.G.L.)
| | - Anne Fox
- Naval Medical Research Unit—Three, Ghana Detachment, Accra 00233, Ghana; (N.A.); Ghana; (A.F.); (E.B.); (S.K.); (C.Y.); (B.A.); (R.E.B.); (D.M.W.); (A.G.L.)
| | - Noah Obeng-Nkrumah
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra 00233, Ghana;
| | - Labi Appiah-Korang
- Department of Microbiology, Korle-Bu Teaching Hospital, Accra 00233, Ghana;
| | - Eric Behene
- Naval Medical Research Unit—Three, Ghana Detachment, Accra 00233, Ghana; (N.A.); Ghana; (A.F.); (E.B.); (S.K.); (C.Y.); (B.A.); (R.E.B.); (D.M.W.); (A.G.L.)
| | - Selassie Kumordjie
- Naval Medical Research Unit—Three, Ghana Detachment, Accra 00233, Ghana; (N.A.); Ghana; (A.F.); (E.B.); (S.K.); (C.Y.); (B.A.); (R.E.B.); (D.M.W.); (A.G.L.)
| | - Clara Yeboah
- Naval Medical Research Unit—Three, Ghana Detachment, Accra 00233, Ghana; (N.A.); Ghana; (A.F.); (E.B.); (S.K.); (C.Y.); (B.A.); (R.E.B.); (D.M.W.); (A.G.L.)
| | - Bright Agbodzi
- Naval Medical Research Unit—Three, Ghana Detachment, Accra 00233, Ghana; (N.A.); Ghana; (A.F.); (E.B.); (S.K.); (C.Y.); (B.A.); (R.E.B.); (D.M.W.); (A.G.L.)
| | - Ronald Essah Bentil
- Naval Medical Research Unit—Three, Ghana Detachment, Accra 00233, Ghana; (N.A.); Ghana; (A.F.); (E.B.); (S.K.); (C.Y.); (B.A.); (R.E.B.); (D.M.W.); (A.G.L.)
| | - Rhodalyn Tagoe
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra 00233, Ghana; (J.B.); (R.T.); (B.K.A.T.); (F.O.)
| | - Blessing Kofi Adu Tabi
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra 00233, Ghana; (J.B.); (R.T.); (B.K.A.T.); (F.O.)
| | - Felicia Owusu
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra 00233, Ghana; (J.B.); (R.T.); (B.K.A.T.); (F.O.)
- Naval Medical Research Unit—Three, Ghana Detachment, Accra 00233, Ghana; (N.A.); Ghana; (A.F.); (E.B.); (S.K.); (C.Y.); (B.A.); (R.E.B.); (D.M.W.); (A.G.L.)
| | - Nicholas T. K. D. Dayie
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra 00233, Ghana; (N.T.K.D.D.); (E.S.D.)
| | - Eric S. Donkor
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra 00233, Ghana; (N.T.K.D.D.); (E.S.D.)
| | - Josephine Nsaful
- Department of Surgery, Korle-bu Teaching Hospital, Accra 00233, Ghana;
| | - Kwaku Asah-Opoku
- Department of Obstetrics and Gynaecology, University of Ghana Medical School, University of Ghana, Accra 00233, Ghana;
| | - Edward Nyarko
- 37 Military Hospital, Accra 00233, Ghana; (E.N.); (E.A.)
| | - Edward Asumanu
- 37 Military Hospital, Accra 00233, Ghana; (E.N.); (E.A.)
| | - Anders Rhod Larsen
- Statens Serum Institut, Department of Bacteria, Parasites and Fungi, Reference Laboratory for Antimicrobial Resistance, Artillerivej 5, DK-2300 Copenhagen, Denmark;
| | - David M. Wolfe
- Naval Medical Research Unit—Three, Ghana Detachment, Accra 00233, Ghana; (N.A.); Ghana; (A.F.); (E.B.); (S.K.); (C.Y.); (B.A.); (R.E.B.); (D.M.W.); (A.G.L.)
| | - Andrew G. Letizia
- Naval Medical Research Unit—Three, Ghana Detachment, Accra 00233, Ghana; (N.A.); Ghana; (A.F.); (E.B.); (S.K.); (C.Y.); (B.A.); (R.E.B.); (D.M.W.); (A.G.L.)
| |
Collapse
|
21
|
Holten Møller C, Andersson M, Rhod Larsen A, Petersen A, Mølbak K, Koch A. Risk of hospitalization and death within 2 years after methicillin-resistant Staphylococcus aureus (MRSA) diagnosis in persons colonized or infected with livestock and non-livestock-associated MRSA-A nationwide register-based cohort study. Zoonoses Public Health 2020; 67:814-822. [PMID: 32949111 DOI: 10.1111/zph.12765] [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: 09/04/2019] [Revised: 06/09/2020] [Accepted: 08/16/2020] [Indexed: 12/01/2022]
Abstract
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) CC398 has emerged in humans throughout Europe and the USA during the last decade and is associated with the spread of LA-MRSA CC398 in production animals. In this study, we investigated the risk of subsequent hospitalization with an S. aureus-related diagnosis and death within the first 2 years after MRSA diagnosis. The study included 7,521 carriers of MRSA, an age-matched reference population of 376,041 individuals and 7,607 patients infected with MRSA. Hazard ratios (HR) for hospitalization with an S. aureus-related diagnosis were 4.09 (95% CI: 2.78-6.00) and for death 1.21 (95% CI: 0.80-1.83) in LA-MRSA CC398 carriers compared with the reference population. Comparing carriers of LA-MRSA CC398 and non-CC398 MRSA, HR for hospitalization was 0.61 (95% CI: 0.37-0.99) and death 0.25 (95% CI: 0.16-0.40), respectively. Patients initially diagnosed with LA-MRSA CC398 or non-CC398 MRSA infection differed from MRSA carriers in terms of older age, higher Charlson comorbidity index score and longer hospital stays. HR for subsequent hospitalization and death was similar regardless having infection with LA-MRSA CC398 or non-CC398 MRSA at the time of MRSA diagnosis. We established that MRSA CC398 carriers have a lower risk of hospitalization and death up to 2 years after MRSA diagnosis than non-CC398 MRSA carriers do. In contrast, MRSA carriage, regardless the MRSA strain is a burden in terms of hospitalization and death when compared to the background reference population. Further, we established that there are no differences in risk of subsequent hospitalization and death in patients initially diagnosed with MRSA CC398 or non-CC398 MRSA infection. We suggest that public health surveillance of MRSA clearly needs to distinguish between carriage and infection as well as strain type before any inference from number of cases to disease burden is made.
Collapse
Affiliation(s)
- Camilla Holten Møller
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Mikael Andersson
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- National Reference Laboratory for Antimicrobial Resistance, Statens Serum Institut, Copenhagen, Denmark
| | - Andreas Petersen
- National Reference Laboratory for Antimicrobial Resistance, Statens Serum Institut, Copenhagen, Denmark
| | - Kåre Mølbak
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark.,Institute of Veterinary and Animal Sciences, Faculty of Health, University of Copenhagen, Denmark
| | - Anders Koch
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
22
|
Møller JK, Larsen AR, Østergaard C, Møller CH, Kristensen MA, Larsen J. International travel as source of a hospital outbreak with an unusual meticillin-resistant Staphylococcus aureus clonal complex 398, Denmark, 2016. ACTA ACUST UNITED AC 2020; 24. [PMID: 31640842 PMCID: PMC6807253 DOI: 10.2807/1560-7917.es.2019.24.42.1800680] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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] [Indexed: 12/16/2022]
Abstract
In May 2016, an unusual outbreak with the Panton-Valentine leukocidin-positive human variant of meticillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 occurred among mothers and infants in the maternity unit of a Danish hospital. MRSA sharing genotypic and phenotypic characteristics was confirmed in 36 cases, including 26 patients, nine household members and a healthcare worker (HCW) who had contact with all the patients. The national MRSA database contained 37 seemingly unlinked MRSA cases whose isolates shared the same genotypic and phenotypic characteristics as the outbreak strain. Whole genome sequencing showed that three of these isolates clustered together with the 36 outbreak isolates, suggesting spread outside the hospital. The HCW and 21 of 37 cases from the national MRSA database had links to south-eastern Asia, where the outbreak strain is endemic. These findings suggest that the HCW acquired the outbreak strain while travelling in south-eastern Asia and then introduced it into the hospital; from there, it spread within the patients’ households and into the community. Screening of travellers returning from countries with high levels of MRSA could be an important intervention to prevent spread of these bacteria into hospitals via patients or HCWs.
Collapse
Affiliation(s)
- Jens Kjølseth Møller
- Institute of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.,Department of Clinical Microbiology, Lillebælt Hospital, Vejle, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Claus Østergaard
- Department of Clinical Microbiology, Lillebælt Hospital, Vejle, Denmark
| | - Camilla Holten Møller
- Department of Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | | | - Jesper Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
23
|
Mellergaard M, Høgh RI, Lund A, Aldana BI, Guérillot R, Møller SH, Hayes AS, Panagiotopoulou N, Frimand Z, Jepsen SD, Hansen CHF, Andresen L, Larsen AR, Peleg AY, Stinear TP, Howden BP, Waagepetersen HS, Frees D, Skov S. Staphylococcus aureus induces cell-surface expression of immune stimulatory NKG2D ligands on human monocytes. J Biol Chem 2020; 295:11803-11821. [PMID: 32605922 PMCID: PMC7450114 DOI: 10.1074/jbc.ra120.012673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 01/21/2020] [Revised: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
Staphylococcus aureus is among the leading causes of bacterial infections worldwide. The pathogenicity and establishment of S. aureus infections are tightly linked to its ability to modulate host immunity. Persistent infections are often associated with mutant staphylococcal strains that have decreased susceptibility to antibiotics; however, little is known about how these mutations influence bacterial interaction with the host immune system. Here, we discovered that clinical S. aureus isolates activate human monocytes, leading to cell-surface expression of immune stimulatory natural killer group 2D (NKG2D) ligands on the monocytes. We found that expression of the NKG2D ligand ULBP2 (UL16-binding protein 2) is associated with bacterial degradability and phagolysosomal activity. Moreover, S. aureus-induced ULBP2 expression was linked to altered host cell metabolism, including increased cytoplasmic (iso)citrate levels, reduced glycolytic flux, and functional mitochondrial activity. Interestingly, we found that the ability of S. aureus to induce ULBP2 and proinflammatory cytokines in human monocytes depends on a functional ClpP protease in S. aureus These findings indicate that S. aureus activates ULBP2 in human monocytes through immunometabolic mechanisms and reveal that clpP inactivation may function as a potential immune evasion mechanism. Our results provide critical insight into the interplay between the host immune system and S. aureus that has evolved under the dual selective pressure of host immune responses and antibiotic treatment. Our discovery of an immune stimulatory pathway consisting of human monocyte-based defense against S. aureus suggests that targeting the NKG2D pathway holds potential for managing persistent staphylococcal infections.
Collapse
Affiliation(s)
- Maiken Mellergaard
- Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Illum Høgh
- Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Astrid Lund
- Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Blanca Irene Aldana
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Romain Guérillot
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sofie Hedlund Møller
- Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ashleigh S Hayes
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nafsika Panagiotopoulou
- Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zofija Frimand
- Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stine Dam Jepsen
- Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Hartmann Friis Hansen
- Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Andresen
- Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Statens Serum Institut, Microbiology and Infection Control, Copenhagen, Denmark
| | - Anton Y Peleg
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Helle S Waagepetersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorte Frees
- Food Safety and Zoonosis, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Skov
- Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
24
|
Niklaus Sieber R, Ravnholt Urth T, Rhod Larsen A, Leo Skov R, Stegger M, Larsen J. Household transmission and host immune evasion factors of LA-MRSA CC398. Access Microbiol 2020. [DOI: 10.1099/acmi.ac2020.po0189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus aureus uses several strategies to evade the host immune reaction including expression of the genes on the immune evasion cluster (IEC), which target the innate immune response, and tarP, which alters the structure of the bacterial wall teichoic acids to avoid binding of host antibodies. IEC is carried on an ΦSa3 prophage, while the tarP gene is found located on diverse prophages. Livestock-associated methicillin-resistant S. aureus of clonal complex 398 (LA-MRSA CC398) typically lacks the IEC, but a number of Danish isolates have been found to carry the elements regardless.
In this study, whole-genome sequences of 96 isolates from humans and 45 isolates from pigs from the North Denmark Region were used to establish a maximum-likelihood phylogeny from core-genome SNPs and to investigate the prevalence of IEC and tarP. Furthermore, epidemiological and national surveillance data were used to investigate household transmission and the prevalence of IEC in LA-MRSA CC398 isolates from the general population. The study documents several independent acquisitions of IEC on distinct ΦSa3 prophages in humans and an almost 3-fold higher human-to-human transmission rate of LA-MRSA CC398 in households with strains carrying IEC than in households with strains lacking it. No such effect was found for tarP, which is widespread among LA-MRSA CC398 isolates from both humans and pigs. Moreover, IEC also seems to promote spread of LA-MRSA CC398 in the general population. Thus, LA-MRSA CC398 is capable of re-adapting to the human host by acquisition of human-specific immune evasion factors encoded on mobile genetic elements.
Collapse
|
25
|
Baig S, Rhod Larsen A, Martins Simões P, Laurent F, Johannesen TB, Lilje B, Tristan A, Schaumburg F, Egyir B, Cirkovic I, Nimmo GR, Spiliopoulou I, Blanc DS, Mernelius S, Moen AEF, David MZ, Andersen PS, Stegger M. Evolution and Population Dynamics of Clonal Complex 152 Community-Associated Methicillin-Resistant Staphylococcus aureus. mSphere 2020; 5:e00226-20. [PMID: 32611695 PMCID: PMC7333568 DOI: 10.1128/msphere.00226-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/12/2020] [Indexed: 11/20/2022] Open
Abstract
Since the late 1990s, changes in the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) were recognized with the emergence of community-associated MRSA (CA-MRSA). CA-MRSA belonging to clonal complex 152 (CC152), carrying the small staphylococcal cassette chromosome mec (SCCmec) type V and encoding the Panton-Valentine leukocidin (PVL), has been observed in Europe. The aim of this study was to investigate its origin, evolution, and dissemination. Whole-genome sequencing was performed on a global collection of 149 CC152 isolates spanning 20 years (93 methicillin-susceptible S. aureus [MSSA] and 56 MRSA isolates). Core genome phylogeny, Bayesian inference, in silico resistance analyses, and genomic characterization were applied. Phylogenetic analysis revealed two major distinct clades, one dominated by MSSA and the other populated only by MRSA. The MSSA isolates were predominately from sub-Saharan Africa, whereas MRSA was almost exclusively from Europe. The European MRSA isolates all harbored an SCCmec type V (5C2&5) element, whereas other SCCmec elements were sporadically detected in MRSA from the otherwise MSSA-dominated clade, including SCCmec types IV (2B), V (5C2), and XIII (9A). In total, 93% of the studied CC152 isolates were PVL positive. Bayesian coalescent inference suggests an emergence of the European CC152-MRSA in the 1990s, while the CC152 lineage dates back to the 1970s. The CA-MRSA CC152 clone mimics the European CC80 CA-MRSA lineage by its emergence from a PVL-positive MSSA ancestor from North Africa or Europe. The CC152 lineage has acquired SCCmec several times, but acquisition of SCCmec type V (5C2&5) seems associated with expansion of MRSA CC152 in Europe.IMPORTANCE Understanding the evolution of CA-MRSA is important in light of the increasing importance of this reservoir in the dissemination of MRSA. Here, we highlight the story of the CA-MRSA CC152 lineage using whole-genome sequencing on an international collection of CC152. We show that the evolution of this lineage is novel and that antibiotic usage may have the potential to select for the phage-encoded Panton-Valentine leukocidin. The diversity of the strains correlated highly to geography, with higher level of resistance observed among the European MRSA isolates. The mobility of the SCCmec element is mandatory for the emergence of novel MRSA lineages, and we show here distinct acquisitions, one of which is linked to the successful clone found throughout Europe today.
Collapse
Affiliation(s)
- Sharmin Baig
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Patrícia Martins Simões
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Laurent
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Berit Lilje
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anne Tristan
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ivana Cirkovic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Graeme R Nimmo
- Pathology Queensland Central Laboratory, Griffith University School of Medicine, Queensland Health, Brisbane, Queensland, Australia
| | - Iris Spiliopoulou
- National Reference Laboratory for Staphylococci, Department of Microbiology, School of Medicine, University of Patras, Patras, Greece
| | - Dominique S Blanc
- Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sara Mernelius
- Laboratory Medicine, Jönköping, Region Jönköping County, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Aina Elisabeth Fossum Moen
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- University of Oslo, Oslo, Norway
| | - Michael Z David
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paal Skytt Andersen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
26
|
Egyir B, Hadjirin NF, Gupta S, Owusu F, Agbodzi B, Adogla-Bessa T, Addo KK, Stegger M, Larsen AR, Holmes MA. Whole-genome sequence profiling of antibiotic-resistant Staphylococcus aureus isolates from livestock and farm attendants in Ghana. J Glob Antimicrob Resist 2020; 22:527-532. [PMID: 32439567 DOI: 10.1016/j.jgar.2020.03.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 03/02/2020] [Accepted: 03/25/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Epidemic methicillin-resistant Staphylococcus aureus (MRSA) clones have been described in Ghana, but so far, no typical livestock-associated MRSA isolates (CC398) have been found. In this study we provide baseline information on antimicrobial resistance, population structure, and virulence gene content of S. aureus isolates from livestock and farm attendants. METHODS Nasal samples were collected from cattle, pigs, goats, sheep, and farm attendants from three farms. Staphylococcus aureus was identified by matrix-assisted laser desorption/ionisation time-of-flight and antimicrobial susceptibility testing was performed using VITEK II (Biomerieux, Marcy l'Etoile, France) and interpreted according to EUCAST guidelines. Whole-genome sequencing was performed using the Illumina, San Diego, CA, USA MiSeq Platform. RESULTS In total, 401 nasal swab samples were obtained from 57 farm attendants, 208 pigs, 30 goats, 26 sheep, and 80 cattle. The S. aureus isolates (n = 25) recovered (farm attendants: n = 10; pigs: n = 8; and goats: n = 7) were frequently resistant to penicillin (68%), tetracycline (44%), and ciprofloxacin (32%); two human isolates were MRSA. Twelve isolates (48%) were multidrug resistant (MDR) (>3 classes). Genome sequencing of the isolates revealed ST152-t355, ST9-t1430, and ST133-t8662 as dominant clones among farm attendants, pigs, and goats, respectively. The two MRSA isolates detected belonged to ST8-t334 and ST152-t355. The scn and sak genes associated with human-adaption were detected in 10 isolates; 9 from humans and 1 from a goat. Typing results provided evidence of a single potential transmission event (t861, PVL-, scn+). CONCLUSION No MRSA was detected among livestock, perhaps because of low intensive farming; however, the relatively high prevalence of MDR isolates may be a result of inappropriate antibiotic usage in Ghanaian livestock production.
Collapse
Affiliation(s)
- Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana.
| | - Nazreen F Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Srishti Gupta
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Felicia Owusu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Bright Agbodzi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Tsatsu Adogla-Bessa
- Livestock and Poultry Research Centre Institute of Agricultural and Consumer Sciences, University of Ghana, Legon, Accra, Ghana
| | - Kennedy Kwasi Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| |
Collapse
|
27
|
Islam MZ, Johannesen TB, Lilje B, Urth TR, Larsen AR, Angen Ø, Larsen J. Investigation of the human nasal microbiome in persons with long- and short-term exposure to methicillin-resistant Staphylococcus aureus and other bacteria from the pig farm environment. PLoS One 2020; 15:e0232456. [PMID: 32353071 PMCID: PMC7192431 DOI: 10.1371/journal.pone.0232456] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 04/15/2020] [Indexed: 12/15/2022] Open
Abstract
Since its emergence in the early 2000s, livestock-associated methicillin-resistant Staphylococcus aureus clonal complex 398 (LA-MRSA CC398) has led to an increasing number of human infections in Denmark and other European countries with industrial pig production. LA-MRSA CC398 is primarily associated with skin infections among pig farm workers but is also increasingly recognized as a cause of life-threatening disease among elderly and immunocompromised people. Pig farm workers may serve as vehicles for the spread of LA-MRSA CC398 and other farm-origin bacteria between farms and into the general population. Yet, little is known about the bacterial community dynamics in pig farm workers and other persons with long- and short-term exposure to the pig farm environment. To gain insight into this, we investigated the nasal microbiomes in pig farm workers during a workweek on four LA-MRSA CC398-positive pig farms, as well as in short-term visitors two hours before, immediately after, and 48 hours after a 1-hour visit to another LA-MRSA CC398-positive pig farm. S. aureus and LA-MRSA CC398 carriage was quantified by means of culture, and the composition of the bacterial communities was investigated through sequencing of the 16S rRNA gene. Pig farm workers often carried LA-MRSA CC398 and other bacteria from the pig farm environment, both at work and at home, although at lower levels at home. In contrast, short-term visitors were subject to a less dramatic and rapidly reversible change in the nasal bacterial community composition. These results suggest that pig farm workers may be an important source of LA-MRSA CC398 and perhaps other pathogens of human and veterinary relevance.
Collapse
Affiliation(s)
- Md Zohorul Islam
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Berit Lilje
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Tinna Ravnholt Urth
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Øystein Angen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jesper Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
- * E-mail:
| |
Collapse
|
28
|
Thorlacius-Ussing L, Sandholdt H, Larsen AR, Petersen A, Benfield T. Age-Dependent Increase in Incidence of Staphylococcus aureus Bacteremia, Denmark, 2008-2015. Emerg Infect Dis 2019; 25. [PMID: 31002300 PMCID: PMC6478196 DOI: 10.3201/eid2505.181733] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
During 2008–2015, overall incidence increased by 50%, with a dramatic increase in persons >80 years of age. Staphylococcus aureus bacteremia (SAB) is a major cause of illness and death worldwide. We analyzed temporal trends of SAB incidence and death in Denmark during 2008–2015. SAB incidence increased 48%, from 20.76 to 30.37 per 100,000 person-years, during this period (p<0.001). The largest change in incidence was observed for persons >80 years of age: a 90% increase in the SAB rate (p<0.001). After adjusting for demographic changes, annual rates increased 4.0% (95% CI 3.0–5.0) for persons <80 years of age, 8.4% (95% CI 7.0–11.0) for persons 80–89 years of age, and 13.0% (95% CI 9.0–17.5) for persons >90 years of age. The 30-day case-fatality rate remained stable at 24%; crude population death rates increased by 53% during 2008–2015 (p<0.001). Specific causes and mechanisms for this rapid increase in SAB incidence among the elderly population remain to be clarified.
Collapse
|
29
|
Sieber RN, Larsen AR, Urth TR, Iversen S, Møller CH, Skov RL, Larsen J, Stegger M. Genome investigations show host adaptation and transmission of LA-MRSA CC398 from pigs into Danish healthcare institutions. Sci Rep 2019; 9:18655. [PMID: 31819134 PMCID: PMC6901509 DOI: 10.1038/s41598-019-55086-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/19/2019] [Indexed: 02/07/2023] Open
Abstract
Over the last decade, an increasing number of infections with livestock-associated methicillin-resistant Staphylococcus aureus of clonal complex 398 (LA-MRSA CC398) in persons without contact to livestock has been registered in Denmark. These infections have been suggested to be the result of repeated spillover of random isolates from livestock into the community. However, other studies also found emerging sub-lineages spreading among humans. Based on genome-wide SNPs and genome-wide association studies (GWAS), we assessed the population structure and genomic content of Danish LA-MRSA CC398 isolates from healthcare-associated infections from 2014 to 2016 (n = 73) and compared these to isolates from pigs in Denmark from 2014 (n = 183). Phylogenetic analyses showed that most human isolates were closely related to and scattered among pig isolates showing that the majority of healthcare-associated infections are the result of repeated spillover from pig farms, even though cases of human-to-human transmission also were identified. GWAS revealed frequent loss of antimicrobial resistance genes and acquisition of human-specific virulence genes in the human isolates showing adaptation in response to changes in selective pressures in different host environments, which over time could lead to the emergence of LA-MRSA CC398 lineages more adapted to human colonization and transmission.
Collapse
Affiliation(s)
- Raphael Niklaus Sieber
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Artillerivej 5, 2300, Copenhagen S, Denmark.
| | - Anders Rhod Larsen
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Tinna Ravnholt Urth
- Statens Serum Institut, Department of Infectious Disease Epidemiology & Prevention, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Søren Iversen
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Camilla Holten Møller
- Statens Serum Institut, Department of Infectious Disease Epidemiology & Prevention, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Robert Leo Skov
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Jesper Larsen
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Marc Stegger
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Artillerivej 5, 2300, Copenhagen S, Denmark.
| |
Collapse
|
30
|
Deplano A, Dodémont M, Denis O, Westh H, Gumpert H, Larsen AR, Larsen J, Kearns A, Pichon B, Layer F, Schulte B, Wolz C, Spiliopoulou I, Brennan G, Empel J, Hryniewicz W, de Lencastre H, Faria NA, Codita I, Sabat AJ, Friedrich AW, Deurenberg RH, Tristan A, Laurent F, Vandenesch F. European external quality assessments for identification, molecular typing and characterization of Staphylococcus aureus. J Antimicrob Chemother 2019; 73:2662-2666. [PMID: 30099486 DOI: 10.1093/jac/dky260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/07/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives We present the results of two European external quality assessments (EQAs) conducted in 2014 and 2016 under the auspices of the Study Group on Staphylococci and Staphylococcal Infections of ESCMID. The objective was to assess the performance of participating centres in characterizing Staphylococcus aureus using their standard in-house phenotypic and genotypic protocols. Methods A total of 11 well-characterized blindly coded S. aureus (n = 9), Staphylococcus argenteus (n = 1) and Staphylococcus capitis (n = 1) strains were distributed to participants for analysis. Species identification, MIC determination, antimicrobial susceptibility testing, antimicrobial resistance and toxin gene detection and molecular typing including spa typing, SCCmec typing and MLST were performed. Results Thirteen laboratories from 12 European countries participated in one EQA or both EQAs. Despite considerable diversity in the methods employed, good concordance (90%-100%) with expected results was obtained. Discrepancies were observed for: (i) identification of the S. argenteus strain; (ii) phenotypic detection of low-level resistance to oxacillin in the mecC-positive strain; (iii) phenotypic detection of the inducible MLSB strain; and (iv) WGS-based detection of some resistance and toxin genes. Conclusions Overall, good concordance (90%-100%) with expected results was observed. In some instances, the accurate detection of resistance and toxin genes from WGS data proved problematic, highlighting the need for validated and internationally agreed-on bioinformatics pipelines before such techniques are implemented routinely by microbiology laboratories. We strongly recommend all national reference laboratories and laboratories acting as referral centres to participate in such EQA initiatives.
Collapse
Affiliation(s)
- Ariane Deplano
- Centre National de Référence S. aureus, Hôpital Erasme - Université Libre de Bruxelles (ULB), 808 Route de Lennik, Bruxelles, Belgium
| | - Magali Dodémont
- Centre National de Référence S. aureus, Hôpital Erasme - Université Libre de Bruxelles (ULB), 808 Route de Lennik, Bruxelles, Belgium
| | - Olivier Denis
- Centre National de Référence S. aureus, Hôpital Erasme - Université Libre de Bruxelles (ULB), 808 Route de Lennik, Bruxelles, Belgium
| | - Henrik Westh
- MRSA Knowledge Center, Hvidovre Hospital, Kettegard Alle 30, Hvidrove, Denmark.,Institute of Clinical Medicine, Faculty of Medicine and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heidi Gumpert
- MRSA Knowledge Center, Hvidovre Hospital, Kettegard Alle 30, Hvidrove, Denmark
| | - Anders Rhod Larsen
- National Reference Laboratory for Antimicrobial Resistance and Staphylococci, Statens Serum Institut, Artllerivej 5, Copenhagen, Denmark
| | - Jesper Larsen
- National Reference Laboratory for Antimicrobial Resistance and Staphylococci, Statens Serum Institut, Artllerivej 5, Copenhagen, Denmark
| | - Angela Kearns
- Staphylococcus Reference Service, National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Bruno Pichon
- Staphylococcus Reference Service, National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Franziska Layer
- Nationale referenzzeebtrum fûr Staphylokokken, Robert Koch Institute, Burgstraße 37, Wernigerode, Germany
| | - Berit Schulte
- Institute für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, Germany
| | - Christiane Wolz
- Institute für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, Germany
| | - Iris Spiliopoulou
- National Staphylococcal Reference Laboratory, Department of Microbiology, School of Medicine, University of Patras, Rion, Patras, Greece
| | - Gráinne Brennan
- National MRSA Reference Laboratory, St James's Hospital, James's Street, Dublin, Ireland
| | - Joanna Empel
- Department of Epidemiology and Clinical Microbiology, Narodowy Instytut Leków, Chelmska 30/34, Warsaw, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, Narodowy Instytut Leków, Chelmska 30/34, Warsaw, Poland
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal.,Laboratory of Microbiology & Infectious Diseases, The Rockefeller University, 1230 York Ave., New York, NY, USA
| | - Nuno Alexandre Faria
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal.,Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Irina Codita
- Cantazuno National Institute of Research, Staphylococcus Reference Laboratory, INC Cantacuzino Splaiul Independentei 103, Bucarest, Romania
| | - Artur J Sabat
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, RB Groningen, The Netherlands
| | - Alexander W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, RB Groningen, The Netherlands
| | - Ruud H Deurenberg
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, RB Groningen, The Netherlands
| | - Anne Tristan
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, 103 Grande Rue de la Croix Rousse, Lyon, France
| | - Frédéric Laurent
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, 103 Grande Rue de la Croix Rousse, Lyon, France
| | - François Vandenesch
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, 103 Grande Rue de la Croix Rousse, Lyon, France
| |
Collapse
|
31
|
Harrison EM, Ba X, Coll F, Blane B, Restif O, Carvell H, Köser CU, Jamrozy D, Reuter S, Lovering A, Gleadall N, Bellis KL, Uhlemann AC, Lowy FD, Massey RC, Grilo IR, Sobral R, Larsen J, Rhod Larsen A, Vingsbo Lundberg C, Parkhill J, Paterson GK, Holden MTG, Peacock SJ, Holmes MA. Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus. Nat Microbiol 2019; 4:1680-1691. [PMID: 31235959 PMCID: PMC7611363 DOI: 10.1038/s41564-019-0471-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/26/2019] [Indexed: 01/04/2023]
Abstract
Antibiotic resistance in bacterial pathogens threatens the future of modern medicine. One such resistant pathogen is methicillin-resistant Staphylococcus aureus (MRSA), which is resistant to nearly all β-lactam antibiotics, limiting treatment options. Here, we show that a significant proportion of MRSA isolates from different lineages, including the epidemic USA300 lineage, are susceptible to penicillins when used in combination with β-lactamase inhibitors such as clavulanic acid. Susceptibility is mediated by a combination of two different mutations in the mecA promoter region that lowers mecA-encoded penicillin-binding protein 2a (PBP2a) expression, and in the majority of isolates by either one of two substitutions in PBP2a (E246G or M122I) that increase the affinity of PBP2a for penicillin in the presence of clavulanic acid. Treatment of S. aureus infections in wax moth and mouse models shows that penicillin/β-lactamase inhibitor susceptibility can be exploited as an effective therapeutic choice for 'susceptible' MRSA infection. Finally, we show that isolates with the PBP2a E246G substitution have a growth advantage in the presence of penicillin but the absence of clavulanic acid, which suggests that penicillin/β-lactamase susceptibility is an example of collateral sensitivity (resistance to one antibiotic increases sensitivity to another). Our findings suggest that widely available and currently disregarded antibiotics could be effective in a significant proportion of MRSA infections.
Collapse
Affiliation(s)
- Ewan M Harrison
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Francesc Coll
- London School of Hygiene and Tropical Medicine, London, UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Henry Carvell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Andrew Lovering
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | | | | | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Franklin D Lowy
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Inês R Grilo
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Rita Sobral
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Gavin K Paterson
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Sharon J Peacock
- Wellcome Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| |
Collapse
|
32
|
Kristinsdottir I, Haraldsson A, Thorkelsson T, Haraldsson G, Kristinsson KG, Larsen J, Larsen AR, Thors V. MRSA outbreak in a tertiary neonatal intensive care unit in Iceland. Infect Dis (Lond) 2019; 51:815-823. [PMID: 31507231 DOI: 10.1080/23744235.2019.1662083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Introduction: Preventing the spread of methicillin-resistant Staphylococcus aureus (MRSA) and understanding the pathophysiology and transmission is essential. This study describes an MRSA outbreak in a neonatal intensive care unit in Reykjavik, Iceland at a time where no screening procedures were active. Materials and methods: After isolating MRSA in the neonatal intensive care unit in 2015, neonates, staff members and parents of positive patients were screened and environmental samples collected. The study period was from 14 April 2015 until 31 August 2015. Antimicrobial susceptibility testing, spa-typing and whole genome sequencing were done on MRSA isolates. Results: During the study period, 96/143 admitted patients were screened for colonization. Non-screened infants had short admissions not including screening days. MRSA was isolated from nine infants and seven parents. All tested staff members were negative. Eight infants and six parents carried MRSA ST30-IVc with spa-type t253 and one infant and its parent carried MRSA CC9-IVa (spa-type t4845) while most environmental samples were MRSA CC9-IVa (spa-type t4845). Whole genome sequencing revealed close relatedness between all ST30-IVc and CC9-IVa isolates, respectively. All colonized infants received decolonization treatment, but 3/9 were still positive when last sampled. Discussion: The main outbreak source was a single MRSA ST30-IVc (spa-type t253), isolated for the first time in Iceland. A new CC9-IVa (spa-type t4845) was also identified, most abundant on environmental surfaces but only in one patient. The reason for the differences in the epidemiology of the two strains is not clear. The study highlights a need for screening procedures in high-risk settings and guidelines for neonatal decolonization.
Collapse
Affiliation(s)
| | - Asgeir Haraldsson
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Children's Hospital Iceland, Landspitali University Hospital , Reykjavík , Iceland
| | - Thordur Thorkelsson
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Children's Hospital Iceland, Landspitali University Hospital , Reykjavík , Iceland
| | - Gunnsteinn Haraldsson
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Department of Clinical Microbiology, Landspitali University Hospital , Reykjavík , Iceland
| | - Karl G Kristinsson
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Department of Clinical Microbiology, Landspitali University Hospital , Reykjavík , Iceland
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institute , Copenhagen , Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institute , Copenhagen , Denmark
| | - Valtyr Thors
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Children's Hospital Iceland, Landspitali University Hospital , Reykjavík , Iceland
| |
Collapse
|
33
|
Becker K, Schaumburg F, Kearns A, Larsen AR, Lindsay JA, Skov RL, Westh H. Implications of identifying the recently defined members of the Staphylococcus aureus complex S. argenteus and S. schweitzeri: a position paper of members of the ESCMID Study Group for Staphylococci and Staphylococcal Diseases (ESGS). Clin Microbiol Infect 2019; 25:1064-1070. [PMID: 30872103 DOI: 10.1016/j.cmi.2019.02.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [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: 12/31/2018] [Revised: 02/18/2019] [Accepted: 02/21/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Staphylococcus argenteus and Staphylococcus schweitzeri, previously known as divergent Staphylococcus aureus clonal lineages, have been recently established as novel, difficult-to-delimit, coagulase-positive species within the S. aureus complex. Methicillin-resistant strains of S. argenteus are known from Australia and the UK. Knowledge of their epidemiology, medical significance and transmission risk is limited and partly contradictory, hampering definitive recommendations. There is mounting evidence that the pathogenicity of S. argenteus is similar to that of 'classical' S. aureus, while as yet no S. schweitzeri infections have been reported. AIM To provide decision support on whether and how to distinguish and report both species. SOURCES PubMed, searched for S. argenteus and S. schweitzeri. CONTENT This position paper reviews the main characteristics of both species and draws conclusions for microbiological diagnostics and surveillance as well as infection prevention and control measures. IMPLICATIONS We propose not distinguishing within the S. aureus complex for routine reporting purposes until there is evidence that pathogenicity or clinical outcome differ markedly between the different species. Primarily for research purposes, suitably equipped laboratories are encouraged to differentiate between S. argenteus and S. schweitzeri. Caution is urged if these novel species are explicitly reported. In such cases, a specific comment should be added (i.e. 'member of the S.aureus complex') to prevent confusion with less- or non-pathogenic staphylococci. Prioritizing aspects of patient safety, methicillin-resistant isolates should be handled as recommended for methicillin-resistant Staphylococcus aureus (MRSA). In these cases, the clinician responsible should be directly contacted and informed by the diagnosing microbiological laboratory, as they would be for MRSA. Research is warranted to clarify the epidemiology, clinical impact and implications for infection control of such isolates.
Collapse
Affiliation(s)
- K Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
| | - F Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - A Kearns
- HCAI and AMR Division, National Infection Service, Public Health England, London, UK
| | - A R Larsen
- National Center for Antimicrobial and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - J A Lindsay
- Institute of Infection and Immunity, St George's, University of London, UK
| | - R L Skov
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - H Westh
- Department of Clinical Microbiology, Hvidovre Hospital, University of Copenhagen, Denmark
| |
Collapse
|
34
|
Thorlacius-Ussing L, Sandholdt H, Larsen AR, Petersen A, Benfield T. Age-Dependent Increase in Incidence of Staphylococcus aureus Bacteremia, Denmark, 2008–2015. Emerg Infect Dis 2019. [DOI: 10.3201/eid2505.181773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
35
|
Uhre ML, Gotland N, Sandholdt H, Mejer N, Petersen A, Rhod Larsen A, Benfield T. Increased risk of diabetes mellitus five years after an episode of Staphylococcus aureus bacteraemia. Infect Dis (Lond) 2019; 51:512-518. [PMID: 31012770 DOI: 10.1080/23744235.2019.1602284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Diabetes mellitus is a risk factor for infection with Staphylococcus aureus, but it is unclear whether S. aureus infection is a prediabetic condition. Methods: Nationwide population-based matched cohort study. Incidence rate and ratio with 95% confidence interval of diabetes were estimated by negative binomial regression. Results: Of 19,988 individuals with S. aureus bacteraemia and 185,579 population comparators, 667 and 4974 had a primary diagnose of diabetes within five years after discharge of S. aureus bacteraemia corresponding to a more than double risk of diabetes (adjusted incidence rate ratio 2.28 (95% confidence interval: 2.10-2.46)). Other factors associated with an increased risk of diabetes during follow-up were male sex, increasing age and level of comorbidity. Of the S. aureus bacteraemia and population cohort, 422 (2.11%) and 4048 (2.18%), respectively, developed diabetes without complications, while 245 (1.23%) and 926 (0.50%), respectively, developed diabetes with complications. Rates of diabetes without complication were increased for individuals in the S. aureus bacteraemia cohort compared to the population cohort within the first two years after which rates were comparable while rates of diabetes with complications remained higher throughout the five year follow-up period compared to the population cohort. Conclusions: The risk of diabetes was markedly increased up to five years after S. aureus bacteraemia compared to a population cohort. In addition to screening for diabetes during hospital admittance, screening cases of S. aureus bacteraemia for diabetes in the years following S. aureus bacteraemia may allow for earlier detection of diabetes.
Collapse
Affiliation(s)
- Marie-Louise Uhre
- a Department of Infectious Diseases , Hvidovre Hospital, University of Copenhagen , Hvidovre , Denmark.,b Department of Medicine , Nykoebing Falster Hospital , Nykoebing Falster , Denmark
| | - Nanja Gotland
- a Department of Infectious Diseases , Hvidovre Hospital, University of Copenhagen , Hvidovre , Denmark
| | - Haakon Sandholdt
- a Department of Infectious Diseases , Hvidovre Hospital, University of Copenhagen , Hvidovre , Denmark.,c Clinical Research Centre , Hvidovre Hospital, University of Copenhagen , Hvidovre , Denmark
| | - Niels Mejer
- a Department of Infectious Diseases , Hvidovre Hospital, University of Copenhagen , Hvidovre , Denmark
| | - Andreas Petersen
- d Reference Laboratory for Antimicrobial Resistance and Staphylococci , Statens Serum Institut , Copenhagen , Denmark
| | - Anders Rhod Larsen
- d Reference Laboratory for Antimicrobial Resistance and Staphylococci , Statens Serum Institut , Copenhagen , Denmark
| | - Thomas Benfield
- a Department of Infectious Diseases , Hvidovre Hospital, University of Copenhagen , Hvidovre , Denmark.,e Department of Clinical Medicine, Faculty of Health and Medical Sciences , University of Copenhagen , Copenhagen , Denmark
| |
Collapse
|
36
|
Lilje B, Rasmussen RV, Dahl A, Stegger M, Skov RL, Fowler VG, Ng KL, Kiil K, Larsen AR, Petersen A, Johansen HK, Schønheyder HC, Arpi M, Rosenvinge FS, Korup E, Høst U, Hassager C, Gill SUA, Hansen TF, Johannesen TB, Smit J, Søgaard P, Skytt Andersen P, Eske-Bruun N. Whole-genome sequencing of bloodstream Staphylococcus aureus isolates does not distinguish bacteraemia from endocarditis. Microb Genom 2019; 3. [PMID: 29208121 PMCID: PMC5729915 DOI: 10.1099/mgen.0.000138] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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] [Indexed: 01/16/2023] Open
Abstract
Most Staphylococcus aureus isolates can cause invasive disease given the right circumstances, but it is unknown if some isolates are more likely to cause severe infections than others. S. aureus bloodstream isolates from 120 patients with definite infective endocarditis and 121 with S. aureus bacteraemia without infective endocarditis underwent whole-genome sequencing. Genome-wide association analysis was performed using a variety of bioinformatics approaches including SNP analysis, accessory genome analysis and k-mer based analysis. Core and accessory genome analyses found no association with either of the two clinical groups. In this study, the genome sequences of S. aureus bloodstream isolates did not discriminate between bacteraemia and infective endocarditis. Based on our study and the current literature, it is not convincing that a specific S. aureus genotype is clearly associated to infective endocarditis in patients with S. aureus bacteraemia.
Collapse
Affiliation(s)
- Berit Lilje
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Rasmus Vedby Rasmussen
- 2Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Copenhagen, Denmark
| | - Anders Dahl
- 2Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Copenhagen, Denmark
| | - Marc Stegger
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Robert Leo Skov
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Vance G Fowler
- 3Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Kim Lee Ng
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Kristoffer Kiil
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Andreas Petersen
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Helle Krogh Johansen
- 4Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Henrik Carl Schønheyder
- 5Department of Clinical Microbiology, Aalborg University Hospital, Clinical Institute, Aalborg University, Aalborg, Denmark
| | - Magnus Arpi
- 6Department of Clinical Microbiology, Copenhagen University Hospital, Herlev-Gentofte, Herlev, Denmark
| | | | - Eva Korup
- 8Department of Cardiology, Aalborg University Hospital, Aalborg, Denmark
| | - Ulla Høst
- 2Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Copenhagen, Denmark
| | - Christian Hassager
- 9Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Thomas Fritz Hansen
- 2Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Copenhagen, Denmark
| | - Thor Bech Johannesen
- 2Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Copenhagen, Denmark
| | - Jesper Smit
- 11Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Peter Søgaard
- 12Department of Cardiology, Clinical Institute, Aalborg University, Aalborg University Hospital, Aalborg, Denmark
| | - Paal Skytt Andersen
- 13Department of Animal and Veterinary Sciences, University of Copenhagen, Copenhagen, Denmark.,14Translational Genomics North, Flagstaff, USA.,1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Niels Eske-Bruun
- 15Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Clinical Institute, Aalborg University, Copenhagen, Aalborg, Denmark
| |
Collapse
|
37
|
Angen Ø, Skade L, Urth TR, Andersson M, Bækbo P, Larsen AR. Controlling Transmission of MRSA to Humans During Short-Term Visits to Swine Farms Using Dust Masks. Front Microbiol 2019; 9:3361. [PMID: 30705674 PMCID: PMC6345077 DOI: 10.3389/fmicb.2018.03361] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 03/02/2018] [Accepted: 12/31/2018] [Indexed: 11/13/2022] Open
Abstract
The aim of the investigation was to determine the protective effect of wearing dust masks to prevent Methicillin-resistant Staphylococcus aureus (MRSA) contamination during a short-term visit in a MRSA-positive swine farm. A total of 118 human volunteers were randomly allocated to a group wearing masks and to the control group. On average, 9% of the participants wearing masks were MRSA-positive when leaving the farm compared to 62% of the participants not wearing masks. At day 1, 2, and 7 after the farm visit, none of those wearing masks were MRSA-positive. An odds ratio of 18.9 (CI: 6.4-56.2) for being MRSA-positive was found for those not wearing masks compared to those wearing masks when including the farm as random effect. None of the covariates (gender, age, and smoking) influenced the OR for being MRSA-positive when leaving the farm. This study shows that the use of dust masks gives a significant protection against nasal MRSA contamination after a short-term visit to a swine farm. In addition, 106 volunteers not wearing masks were investigated in order to provide an estimate of a contamination dose of airborne MRSA. Due to the high variation in the MRSA measurements, it was not possible to establish a stable estimate for this. Out of the 106 volunteers not wearing masks, 6, 7, and 3% tested MRSA-positive 1, 2, and 7 days after the farm visit, respectively.
Collapse
Affiliation(s)
- Øystein Angen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Lotte Skade
- SEGES Danish Pig Research Centre, Kjellerup, Denmark
| | - Tinna Ravnholt Urth
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mikael Andersson
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Poul Bækbo
- SEGES Danish Pig Research Centre, Kjellerup, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
38
|
Scott WK, Medie FM, Ruffin F, Sharma-Kuinkel BK, Cyr DD, Guo S, Dykxhoorn DM, Skov RL, Bruun NE, Dahl A, Lerche CJ, Petersen A, Larsen AR, Lauridsen TK, Johansen HK, Ullum H, Sørensen E, Hassager C, Bundgaard H, Schønheyder HC, Torp-Pedersen C, Østergaard LB, Arpi M, Rosenvinge F, Erikstrup LT, Chehri M, Søgaard P, Andersen PS, Fowler VG. Human genetic variation in GLS2 is associated with development of complicated Staphylococcus aureus bacteremia. PLoS Genet 2018; 14:e1007667. [PMID: 30289878 PMCID: PMC6192642 DOI: 10.1371/journal.pgen.1007667] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 10/17/2018] [Accepted: 08/29/2018] [Indexed: 12/30/2022] Open
Abstract
The role of host genetic variation in the development of complicated Staphylococcus aureus bacteremia (SAB) is poorly understood. We used whole exome sequencing (WES) to examine the cumulative effect of coding variants in each gene on risk of complicated SAB in a discovery sample of 168 SAB cases (84 complicated and 84 uncomplicated, frequency matched by age, sex, and bacterial clonal complex [CC]), and then evaluated the most significantly associated genes in a replication sample of 240 SAB cases (122 complicated and 118 uncomplicated, frequency matched for age, sex, and CC) using targeted sequence capture. In the discovery sample, gene-based analysis using the SKAT-O program identified 334 genes associated with complicated SAB at p<3.5 x 10−3. These, along with eight biologically relevant candidate genes were examined in the replication sample. Gene-based analysis of the 342 genes in the replication sample using SKAT-O identified one gene, GLS2, significantly associated with complicated SAB (p = 1.2 x 10−4) after Bonferroni correction. In Firth-bias corrected logistic regression analysis of individual variants, the strongest association across all 10,931 variants in the replication sample was with rs2657878 in GLS2 (p = 5 x 10−4). This variant is strongly correlated with a missense variant (rs2657879, p = 4.4 x 10−3) in which the minor allele (associated here with complicated SAB) has been previously associated with lower plasma concentration of glutamine. In a microarray-based gene-expression analysis, individuals with SAB exhibited significantly lower expression levels of GLS2 than healthy controls. Similarly, Gls2 expression is lower in response to S. aureus exposure in mouse RAW 264.7 macrophage cells. Compared to wild-type cells, RAW 264.7 cells with Gls2 silenced by CRISPR-Cas9 genome editing have decreased IL1-β transcription and increased nitric oxide production after S. aureus exposure. GLS2 is an interesting candidate gene for complicated SAB due to its role in regulating glutamine metabolism, a key factor in leukocyte activation. Complications from bloodstream infection with Staphylococcus aureus (S. aureus) are important causes of hospitalization, significant illness, and death. The causes of these complications are not well understood, but likely involve genetic factors rendering people more susceptible to such infections, differences in the bacteria that cause the infection, and the interactions between them. We examined the parts of the human genome that code for proteins to find variations that were more common in people with complicated S. aureus bacteremia (SAB), and identified one gene, called GLS2, in which variation is more common in complicated SAB cases than uncomplicated cases. Expression of GLS2 is lower in people with SAB than controls and in mouse white blood cells exposed to S. aureus. GLS2 encodes a protein that regulates the metabolism of glutamine, a regulatory process that activates white blood cells. These cells are very important in the immune response to S. aureus infection, and therefore genetic variants that might influence their growth are important potential genetic risk factors for complicated SAB.
Collapse
Affiliation(s)
- William K. Scott
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- * E-mail: (WKS); (PSA); (VGF)
| | - Felix Mba Medie
- Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, Durham, NC, United States of America
| | - Felicia Ruffin
- Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, Durham, NC, United States of America
| | - Batu K. Sharma-Kuinkel
- Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, Durham, NC, United States of America
| | - Derek D. Cyr
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Robert L. Skov
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Niels E. Bruun
- Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Anders Dahl
- Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Denmark
| | - Christian J. Lerche
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Andreas Petersen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Helle Krogh Johansen
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Henrik Ullum
- Department of Clinical Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Christian Hassager
- Department of Cardiology, Rigshospitalet and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Henning Bundgaard
- Department of Cardiology, Rigshospitalet and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Henrik C. Schønheyder
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | - Louise Bruun Østergaard
- Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Denmark
- Clinical Institute, Aalborg University, Aalborg, Denmark
| | - Magnus Arpi
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev-Gentofte, Denmark
| | - Flemming Rosenvinge
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Lise T. Erikstrup
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
| | - Mahtab Chehri
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Peter Søgaard
- Department of Cardiology, Aalborg University Hospital, Aalborg, Denmark
| | - Paal S. Andersen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (WKS); (PSA); (VGF)
| | - Vance G. Fowler
- Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, Durham, NC, United States of America
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, United States of America
- * E-mail: (WKS); (PSA); (VGF)
| |
Collapse
|
39
|
Momoh AH, Kwaga JKP, Bello M, Sackey AKB, Larsen AR. Antibiotic resistance and molecular characteristics of Staphylococcus aureus isolated from backyard-raised pigs and pig workers. Trop Anim Health Prod 2018; 50:1565-1571. [PMID: 29675779 DOI: 10.1007/s11250-018-1596-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 03/18/2017] [Accepted: 04/10/2018] [Indexed: 12/11/2022]
Abstract
Staphylococcus aureus is a commensal and pathogenic bacterium with impact on public health and livestock industry. The study investigated nasal carriage, antibiotic resistance, and molecular characterization of S. aureus in pigs and pig workers. Nasal swabs from 300 backyard-raised pigs and 101 pig workers were used for the study. Resulting isolates were confirmed using MALDI-TOF MS, tested for antibiotic resistance, and three different multiplex PCRs were used to detect enterotoxin, mecA, spaA, scn, and pvl genes. spa typing was used to annotate the isolates into MLST clonal complexes (CC). Structured questionnaire was used to access possible risk factors for S. aureus carriage. The prevalence of S. aureus in pigs and pig workers were 5.3 and 12.9%, respectively. The isolates were resistant to beta-lactams (97%), tetracycline (62%), sulfonamide (52%), aminoglycoside (20.6%), fluoroquinolone (24%), and mupirocin (3.4%). Twenty seven (93%) of the isolates carried scn, 7(24%) pvl, and 12 (41%) enterotoxin genes, respectively. Questionnaire survey showed medical-related occupation of household members was associated (p < 0.5) with S. aureus carriage. This study suggests the presence of human multidrug resistant strains of S. aureus, high carriage of pvl, and enterotoxin genes, and CC5, CC15, and CC152 were the CC-groups shared among pigs and pig workers.
Collapse
Affiliation(s)
- Asabe Halimat Momoh
- Department of Veterinary Public Health and Preventive Medicine, Ahmadu Bello University, Zaria, Nigeria.
| | - Jacob K P Kwaga
- Department of Veterinary Public Health and Preventive Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Mohammed Bello
- Department of Veterinary Public Health and Preventive Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Anthony K B Sackey
- Department of Veterinary Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Anders Rhod Larsen
- National Center for Antimicrobial and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
40
|
Baig S, Johannesen TB, Overballe-Petersen S, Larsen J, Larsen AR, Stegger M. Novel SCCmec type XIII (9A) identified in an ST152 methicillin-resistant Staphylococcus aureus. Infect Genet Evol 2018; 61:74-76. [PMID: 29567305 DOI: 10.1016/j.meegid.2018.03.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/09/2018] [Accepted: 03/16/2018] [Indexed: 11/17/2022]
Abstract
We identified a novel staphylococcal cassette chromosome mec (SCCmec) element in an ST152 methicillin-resistant Staphylococcus aureus (MRSA) isolate by combining Illumina and MinION sequencing. The element contains a new ccrC allotype designated ccrC2. The mec complex resembles mec class A, but with an altered organization of the genes. The element was acknowledged as novel by the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements (IWG-SCC) and designated SCCmec type XIII (9A).
Collapse
Affiliation(s)
- Sharmin Baig
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Jesper Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark.
| |
Collapse
|
41
|
Larsen J, Sunde M, Islam MZ, Urdahl AM, Barstad AS, Larsen AR, Grøntvedt CA, Angen Ø. Evaluation of a widely used culture-based method for detection of livestock-associated meticillin-resistant Staphylococcus aureus (MRSA), Denmark and Norway, 2014 to 2016. ACTA ACUST UNITED AC 2018; 22:30573. [PMID: 28749335 PMCID: PMC5545765 DOI: 10.2807/1560-7917.es.2017.22.28.30573] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/11/2017] [Indexed: 01/31/2023]
Abstract
We evaluated a widely used culture-based method for detection of livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) in samples collected from pigs and the environment inside pig stables in Denmark and Norway. Selective enrichment in tryptic soy broth containing cefoxitin and aztreonam led to a high ratio of false-negative results (26%; 57/221). On this basis, we recommend reconsidering the use of selective enrichment for detection of LA-MRSA in animal and environmental samples.
Collapse
Affiliation(s)
- Jesper Larsen
- Statens Serum Institut, Copenhagen S, Denmark.,These authors contributed equally as first authors
| | - Marianne Sunde
- These authors contributed equally as first authors.,The Norwegian Veterinary Institute, Oslo, Norway
| | | | | | | | | | | | - Øystein Angen
- Statens Serum Institut, Copenhagen S, Denmark.,The Norwegian Veterinary Institute, Oslo, Norway
| |
Collapse
|
42
|
Feld L, Bay H, Angen Ø, Larsen AR, Madsen AM. Survival of LA-MRSA in Dust from Swine Farms. Ann Work Expo Health 2018; 62:147-156. [PMID: 29365048 PMCID: PMC6788576 DOI: 10.1093/annweh/wxx108] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 10/30/2017] [Accepted: 12/07/2017] [Indexed: 11/24/2022] Open
Abstract
Dust is suspected to be an important factor in transmission of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) between pigs and pig farmers and their families. The aim of this study was to determine the rate of decay for Staphylococcus aureus and LA-MRSA in dust from swine farms. Electrostatic dust fall collectors (EDCs) were used for passive sampling of settling airborne dust in 11 stable sections from six swine farms. Extraction, plating, identification, and enumeration of cultivable S. aureus and LA-MRSA from the EDCs were performed after storage for 0-30 days postsampling. The survival of S. aureus was measured in 196 dust samples from all farms, and data were used to estimate the decay constant λ according to a model for exponential decay: N(t) = N0 × e-λt. The number of S. aureus colonies was up to 600-fold higher than the number of LA-MRSA colonies on MRSA selective agar. The data showed a good fit to the model (λ = 0.13, r2 = 0.86) even with a large difference in initial concentrations of S. aureus between stables. The loads of S. aureus and LA-MRSA in the dust were significantly reduced by storage time, and the half-life was 5 days for both S. aureus and LA-MRSA. In dust samples with high initial concentrations, LA-MRSA and S. aureus could still be cultivated 30 days after sampling. On all farms MRSA isolates belonged to the clonal complex (CC) 398, and at one farm some isolates also belonged to CC30. A screening for other Staphylococcus species in the farm dust revealed 13 different species numerically dominated by Staphylococcus equorum. Based on the exponential decay model, S. equorum had a half-life of 4 days. In conclusion, the presence of MRSA in airborne dust from five of six farms indicates that dust might be an important vehicle for transmission of LA-MRSA. LA-MRSA and S. aureus was found to survive well in farm dust with half-lives of 5 days, and dependent on the initial concentration they could be found in farm dust for weeks. The 99.9% die-off rate was 66 days for LA-MRSA. Thus, farm dust can pose an exposure risk for humans in the farm environment, but also when transported to other environments. On the other hand, the risk will decrease by time. These results provide important knowledge to diminish spread from farm environments to other environments on, e.g., tools or clothing, and in relation to cleaning of emptied LA-MRSA-positive stables.
Collapse
Affiliation(s)
- Louise Feld
- The National Research Center for the Working Environment, Copenhagen Ø, Denmark
| | - Hans Bay
- The National Research Center for the Working Environment, Copenhagen Ø, Denmark
| | | | | | - Anne Mette Madsen
- The National Research Center for the Working Environment, Copenhagen Ø, Denmark
| |
Collapse
|
43
|
Kaya H, Hasman H, Larsen J, Stegger M, Johannesen TB, Allesøe RL, Lemvigh CK, Aarestrup FM, Lund O, Larsen AR. SCC mecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data. mSphere 2018; 3:e00612-17. [PMID: 29468193 PMCID: PMC5812897 DOI: 10.1128/msphere.00612-17] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 12/27/2017] [Indexed: 01/05/2023] Open
Abstract
Typing of methicillin-resistant Staphylococcus aureus (MRSA) is important in infection control and surveillance. The current nomenclature of MRSA includes the genetic background of the S. aureus strain determined by multilocus sequence typing (MLST) or equivalent methods like spa typing and typing of the mobile genetic element staphylococcal cassette chromosome mec (SCCmec), which carries the mecA or mecC gene. Whereas MLST and spa typing are relatively simple, typing of SCCmec is less trivial because of its heterogeneity. Whole-genome sequencing (WGS) provides the essential data for typing of the genetic background and SCCmec, but so far, no bioinformatic tools for SCCmec typing have been available. Here, we report the development and evaluation of SCCmecFinder for characterization of the SCCmec element from S. aureus WGS data. SCCmecFinder is able to identify all SCCmec element types, designated I to XIII, with subtyping of SCCmec types IV (2B) and V (5C2). SCCmec elements are characterized by two different gene prediction approaches to achieve correct annotation, a Basic Local Alignment Search Tool (BLAST)-based approach and a k-mer-based approach. Evaluation of SCCmecFinder by using a diverse collection of clinical isolates (n = 93) showed a high typeability level of 96.7%, which increased to 98.9% upon modification of the default settings. In conclusion, SCCmecFinder can be an alternative to more laborious SCCmec typing methods and is freely available at https://cge.cbs.dtu.dk/services/SCCmecFinder. IMPORTANCE SCCmec in MRSA is acknowledged to be of importance not only because it contains the mecA or mecC gene but also for staphylococcal adaptation to different environments, e.g., in hospitals, the community, and livestock. Typing of SCCmec by PCR techniques has, because of its heterogeneity, been challenging, and whole-genome sequencing has only partially solved this since no good bioinformatic tools have been available. In this article, we describe the development of a new bioinformatic tool, SCCmecFinder, that includes most of the needs for infection control professionals and researchers regarding the interpretation of SCCmec elements. The software detects all of the SCCmec elements accepted by the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements, and users will be prompted if diverging and potential new elements are uploaded. Furthermore, SCCmecFinder will be curated and updated as new elements are found and it is easy to use and freely accessible.
Collapse
Affiliation(s)
- Hülya Kaya
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Rosa Lundbye Allesøe
- Center for Biological Sequence Analysis, Department of Bioinformatics, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Camilla Koldbæk Lemvigh
- Center for Biological Sequence Analysis, Department of Bioinformatics, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Frank Møller Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Bioinformatics, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
44
|
Cirkovic I, Trajkovic J, Hauschild T, Andersen PS, Shittu A, Larsen AR. Nasal and pharyngeal carriage of methicillin-resistant Staphylococcus sciuri among hospitalised patients and healthcare workers in a Serbian university hospital. PLoS One 2017; 12:e0185181. [PMID: 28926634 PMCID: PMC5605001 DOI: 10.1371/journal.pone.0185181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 09/07/2017] [Indexed: 11/19/2022] Open
Abstract
There has been a paucity of data on methicillin-resistant Staphylococcus sciuri (MRSS) epidemiology in European healthcare settings. The aim of the study was to determine the prevalence of nasal and pharyngeal carriage and diversity of MRSS among inpatients and healthcare workers (HCWs) in the largest healthcare centre in Serbia, and to assess performance of different methods for MRSS screening. Nasal and pharyngeal swabs were obtained from 195 patients and 105 HCWs in different departments. Each swab was inoculated directly onto MRSA-ID, oxacillin-resistance screening agar and mannitol salt agar (MSA) with 2 mg/L of oxacillin. After inoculation, each swab was dipped in Mueller-Hinton broth with 6.5% NaCl and after overnight incubation, subcultured onto oxacillin-MSA. Characterisation of isolated MRSS strains was determined by antimicrobial susceptibility testing, PFGE, SCCmec typing and antimicrobial resistance genes detection. MRSS nasal and pharyngeal carriage rate was high (5%) in our hospital and department-variable. PFGE revealed a possible cross-transmission of MRSS between a patient and an HCW, and dissemination across hospital wards. All analysed isolates were multidrug resistant. Fusidic acid resistance was discovered in 93.7% of isolates, but fusA mutations in EF-G and fusB/C genes were not detected. SCCmec regions of MRSS contained elements of classic methicillin-resistant S. aureus type III. Broth enrichment prior to isolation on oxacillin-MSA was superior to direct cultivation on different media with a sensitivity/specificity of 100% and 88.5%, respectively. MRSS is a significant coloniser of patients and HCWs in the hospital. Further research is needed to investigate the clinical significance of the bacterium in our settings.
Collapse
Affiliation(s)
- Ivana Cirkovic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- * E-mail:
| | - Jasmina Trajkovic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Tomasz Hauschild
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland
| | - Paal Skytt Andersen
- Department Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Adebayo Shittu
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Anders Rhod Larsen
- Department Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
45
|
Dupieux C, Kolenda C, Larsen AR, Pichon B, Holmes M, Bes M, Teale C, Dickson E, Hill R, Skov R, Kearns A, Laurent F. Variable performance of four commercial chromogenic media for detection of methicillin-resistant Staphylococcus aureus isolates harbouring mecC. Int J Antimicrob Agents 2017; 50:263-265. [DOI: 10.1016/j.ijantimicag.2017.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/02/2017] [Indexed: 10/19/2022]
|
46
|
Edslev SM, Westh H, Andersen PS, Skov R, Kobayashi N, Bartels MD, Vandenesch F, Petersen A, Worning P, Larsen AR, Stegger M. Identification of a PVL-negative SCCmec-IVa sublineage of the methicillin-resistant Staphylococcus aureus CC80 lineage: understanding the clonal origin of CA-MRSA. Clin Microbiol Infect 2017; 24:273-278. [PMID: 28668467 DOI: 10.1016/j.cmi.2017.06.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 04/03/2017] [Revised: 06/19/2017] [Accepted: 06/21/2017] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Community-acquired (CA) methicillin-resistant Staphylococcus aureus (MRSA) isolates belonging to clonal complex 80 (CC80) are recognized as the European CA-MRSA. The prevailing European CA-MRSA clone carries a type IVc staphylococcal cassette chromosome mec (SCCmec) and expresses Panton-Valentine leukocidin (PVL). Recently, a significant increase of PVL-negative CC80 MRSA has been observed in Denmark. The aim of this study was to examine their genetics and epidemiology, and to compare them to the European CA-MRSA clone in order to understand the emergence of PVL-negative CC80 MRSA. METHODS Phylogenetic analysis of the CC80 S. aureus lineage was conducted from whole-genome sequences of 217 isolates (23 methicillin-susceptible S. aureus and 194 MRSA) from 22 countries. All isolates were further genetically characterized in regard to resistance determinants and PVL carriage, and epidemiologic data were obtained for selected isolates. RESULTS Phylogenetic analysis revealed the existence of three distinct clades of the CC80 lineage: (a) an methicillin-susceptible S. aureus clade encompassing Sub-Saharan African isolates (n = 13); (b) a derived clade encompassing the European CA-MRSA SCCmec-IVc clone (n = 185); and (c) a novel and genetically distinct clade encompassing MRSA SCCmec-IVa isolates (n = 19). All isolates in the novel clade were PVL negative, but carried remnant parts (8-12 kb) of the PVL-encoding prophage ΦSa2 and were susceptible to fusidic acid and kanamycin/amikacin. Geospatial mapping could link these isolates to regions in the Middle East, Asia and South Pacific. CONCLUSIONS This study reports the emergence of a novel CC80 CA-MRSA sublineage, showing that the CC80 lineage is more diverse than previously assumed.
Collapse
Affiliation(s)
- S M Edslev
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - H Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark; Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - P S Andersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark; Division of Pathogen Genomics, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - R Skov
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - N Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - M D Bartels
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - F Vandenesch
- International Center for Infectiology Research, Université Lyon 1, Lyon, France
| | - A Petersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - P Worning
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - A R Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - M Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark; Division of Pathogen Genomics, Translational Genomics Research Institute, Phoenix, AZ, USA.
| |
Collapse
|
47
|
Hansen JE, Larsen AR, Skov RL, Chriél M, Larsen G, Angen Ø, Larsen J, Lassen DCK, Pedersen K. Livestock-associated methicillin-resistant Staphylococcus aureus is widespread in farmed mink (Neovison vison). Vet Microbiol 2017; 207:44-49. [PMID: 28757038 DOI: 10.1016/j.vetmic.2017.05.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 02/28/2017] [Revised: 05/27/2017] [Accepted: 05/29/2017] [Indexed: 10/19/2022]
Abstract
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 is widespread in the Danish pig production with around 90% of herds being positive. Since 2009, cases of CC398 LA-MRSA infections in Danish mink farmers have been observed. The objective of the study was to examine the presence of LA-MRSA in farmed mink. The investigation comprised three different sample types 1) clinical samples from carcasses submitted to the laboratory for diagnostic examination, 2) paws and pharyngeal swabs from healthy animals collected at pelting, and 3) feed samples from mink feed producers. In clinical samples, LA-MRSA was found in 34% of submissions and was most prevalent in samples from paws (33%) and pharynx (17%), followed by nasal and intestinal samples (each 13%), whereas it was never detected in perineal samples. LA-MRSA was found in healthy animals on 40% of the investigated farms, including paw samples (29%) and pharyngeal samples (16%). Twenty out of the 108 feed samples from feed producers were positive for LA-MRSA. The dominant spa-types were t034 and t011 associated to CC398, corresponding to the dominant spa-types detected in the Danish pig production, from which slaughter offal is used for mink feed. The spa-types, the high prevalence of LA-MRSA on paws and in pharynx, and its detection in feed samples, suggest feed as a possible source of LA-MRSA in mink.
Collapse
Affiliation(s)
- Julie Elvekjær Hansen
- National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, DK-1870 Frederiksberg C, Denmark.
| | | | - Robert Leo Skov
- Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - Mariann Chriél
- National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, DK-1870 Frederiksberg C, Denmark
| | - Gitte Larsen
- National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, DK-1870 Frederiksberg C, Denmark
| | - Øystein Angen
- Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - Jesper Larsen
- Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | | | - Karl Pedersen
- National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, DK-1870 Frederiksberg C, Denmark
| |
Collapse
|
48
|
Hansen MLU, Gotland N, Mejer N, Larsen AR, Petersen A, Benfield T. Increased Risk of Incident Diabetes Mellitus 2 Years After Staphylococcus aureus Bacteremia: A Matched Cohort Study. Open Forum Infect Dis 2016. [DOI: 10.1093/ofid/ofw172.153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Nanja Gotland
- Department of Infectious Diseases, Hvidovre University Hospital, Hvidovre, Denmark
| | - Niels Mejer
- Hvidovre University Hospital, Hvidovre, Denmark
| | | | | | - Thomas Benfield
- Department of Infectious Disease, Hvidovre University Hospital, Hvidovre, Denmark
| |
Collapse
|
49
|
Gotland N, Hansen MLU, Mejer N, Skov R, Petersen A, Larsen AR, Benfield T. Increased Risk of Incident Cancer After Staphylococcus aureus Bacteremia: A Matched Cohort Study. Open Forum Infect Dis 2016. [DOI: 10.1093/ofid/ofw172.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nanja Gotland
- Department of Infectious Diseases, Hvidovre University Hospital, Hvidovre, Denmark
| | | | - Niels Mejer
- Hvidovre University Hospital, Hvidovre, Denmark
| | - Robert Skov
- National Center for Antimicrobials and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Thomas Benfield
- Department of Infectious Disease, Hvidovre University Hospital, Hvidovre, Denmark
| |
Collapse
|
50
|
Angen Ø, Stegger M, Larsen J, Lilje B, Kaya H, Pedersen KS, Jakobsen A, Petersen A, Larsen AR. Report of mecC-carrying MRSA in domestic swine. J Antimicrob Chemother 2016; 72:60-63. [PMID: 27650187 PMCID: PMC5161050 DOI: 10.1093/jac/dkw389] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/17/2016] [Accepted: 08/18/2016] [Indexed: 12/21/2022] Open
Abstract
Objectives We unexpectedly identified MRSA isolates carrying mecC (mecC-MRSA) from a Danish swine farm located in eastern Zealand. The objective of the present study was to investigate the origin of these isolates and their genetic relatedness to other mecC-MRSA isolates from Zealand. Methods WGS was used to infer the phylogenetic relationship between 19 identified mecC-MRSA isolates from the swine farm and 34 additional epidemiologically unrelated human isolates from the same geographical region of Denmark. Variations in the accessory genome were investigated by bioinformatics tools, and antibiotic susceptibility profiles were assessed by MIC determination. Results mecC-MRSA was isolated from a domestic swine farm, but not from cattle reared at the same farm. Phylogenetic analysis revealed that all mecC-MRSA isolates from both farm animals and workers formed a separate cluster, whereas human isolates from the same municipality belonged to a closely related cluster. Analysis of the accessory genome supported this relationship. Conclusions To the best of our knowledge, this is the first report of mecC-MRSA isolated from domestic swine. The investigation strongly indicates that transmission of mecC-MRSA has taken place on the swine farm between the farmers and swine. The close clustering of farm isolates and isolates from the same municipality suggests a local transmission of mecC-MRSA.
Collapse
Affiliation(s)
- Ø Angen
- Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - M Stegger
- Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - J Larsen
- Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - B Lilje
- Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - H Kaya
- Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | | | - A Jakobsen
- Ø-Vet, Køberupvej 33, 4700 Næstved, Denmark
| | - A Petersen
- Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - A R Larsen
- Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| |
Collapse
|