1
|
Phylodynamic signatures in the emergence of community-associated MRSA. Proc Natl Acad Sci U S A 2022; 119:e2204993119. [PMID: 36322765 PMCID: PMC9659408 DOI: 10.1073/pnas.2204993119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Community-associated, methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) lineages have emerged in many geographically distinct regions around the world during the past 30 y. Here, we apply consistent phylodynamic methods across multiple community-associated MRSA lineages to describe and contrast their patterns of emergence and dissemination. We generated whole-genome sequencing data for the Australian sequence type (ST) ST93-MRSA-IV from remote communities in Far North Queensland and Papua New Guinea, and the Bengal Bay ST772-MRSA-V clone from metropolitan communities in Pakistan. Increases in the effective reproduction number (R<sub>e</sub>) and sustained transmission (R<sub>e</sub> > 1) coincided with spread of progenitor methicillin-susceptible <i>S. aureus</i> (MSSA) in remote northern Australian populations, dissemination of the ST93-MRSA-IV genotype into population centers on the Australian East Coast, and subsequent importation into the highlands of Papua New Guinea and Far North Queensland. Applying the same phylodynamic methods to existing lineage datasets, we identified common signatures of epidemic growth in the emergence and epidemiological trajectory of community-associated <i>S. aureus</i> lineages from America, Asia, Australasia, and Europe. Surges in R<sub>e</sub> were observed at the divergence of antibiotic-resistant strains, coinciding with their establishment in regional population centers. Epidemic growth was also observed among drug-resistant MSSA clades in Africa and northern Australia. Our data suggest that the emergence of community-associated MRSA in the late 20th century was driven by a combination of antibiotic-resistant genotypes and host epidemiology, leading to abrupt changes in lineage-wide transmission dynamics and sustained transmission in regional population centers.
Collapse
|
2
|
Godijk NG, Bootsma MCJ, Bonten MJM. Transmission routes of antibiotic resistant bacteria: a systematic review. BMC Infect Dis 2022; 22:482. [PMID: 35596134 PMCID: PMC9123679 DOI: 10.1186/s12879-022-07360-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
Background Quantification of acquisition routes of antibiotic resistant bacteria (ARB) is pivotal for understanding transmission dynamics and designing cost-effective interventions. Different methods have been used to quantify the importance of transmission routes, such as relative risks, odds ratios (OR), genomic comparisons and basic reproduction numbers. We systematically reviewed reported estimates on acquisition routes’ contributions of ARB in humans, animals, water and the environment and assessed the methods used to quantify the importance of transmission routes. Methods PubMed and EMBASE were searched, resulting in 6054 articles published up until January 1st, 2019. Full text screening was performed on 525 articles and 277 are included. Results We extracted 718 estimates with S. aureus (n = 273), E. coli (n = 157) and Enterobacteriaceae (n = 99) being studied most frequently. Most estimates were derived from statistical methods (n = 560), mainly expressed as risks (n = 246) and ORs (n = 239), followed by genetic comparisons (n = 85), modelling (n = 62) and dosage of ARB ingested (n = 17). Transmission routes analysed most frequently were occupational exposure (n = 157), travelling (n = 110) and contacts with carriers (n = 83). Studies were mostly performed in the United States (n = 142), the Netherlands (n = 87) and Germany (n = 60). Comparison of methods was not possible as studies using different methods to estimate the same route were lacking. Due to study heterogeneity not all estimates by the same method could be pooled. Conclusion Despite an abundance of published data the relative importance of transmission routes of ARB has not been accurately quantified. Links between exposure and acquisition are often present, but the frequency of exposure is missing, which disables estimation of transmission routes’ importance. To create effective policies reducing ARB, estimates of transmission should be weighed by the frequency of exposure occurrence. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07360-z.
Collapse
Affiliation(s)
- Noortje G Godijk
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
| | - Martin C J Bootsma
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Mathematics, Faculty of Sciences, Utrecht University, Utrecht, The Netherlands
| | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
3
|
Santosaningsih D, Erikawati D, Hakim IA, Santoso S, Hidayat M, Suwenda AH, Puspitasari V, Irhamni I, Kuntaman K, van Arkel ALE, Terlouw LG, Oudenes N, Willemse-Erix D, Snijders SV, Erler NS, Verbrugh HA, Severin JA. Reducing transmission of methicillin-resistant Staphylococcus aureus in a surgical ward of a resource-limited hospital in Indonesia: an intervention study. Infect Prev Pract 2019; 1:100028. [PMID: 34368685 PMCID: PMC8335904 DOI: 10.1016/j.infpip.2019.100028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/25/2019] [Indexed: 11/26/2022] Open
Abstract
Background Methicillin-resistant Staphylococcus aureus (MRSA) is endemic in healthcare settings in Indonesia. Aim To evaluate the effect of a bundle of preventive measures on the transmission and acquisition of MRSA in a surgical ward of a resource-limited hospital in Indonesia. Methods The study consisted of a pre-intervention (7 months), intervention (2 months), and post-intervention phase (5 months) and included screening for MRSA among eligible patients, healthcare workers (HCWs), and the hospital environment. In the intervention phase, a bundle of preventive actions was introduced, comprising: a hand hygiene educational program, cohorting of MRSA-positive patients, decolonization therapy for all MRSA-positive patients and HCWs, and cleaning and disinfection of the ward's innate environment. Hand hygiene compliance was assessed throughout the study period. The primary outcome was the acquisition rate of MRSA among patients per 1,000 patient-days at risk. Clonality of MRSA isolates was determined by Raman spectroscopy and multilocus sequence typing. Findings In total, 1,120 patients were included. Hand hygiene compliance rate rose from 15% pre-intervention to 65% post-intervention (P<0.001). The MRSA acquisition decreased from 9/1,000 patient-days at risk pre-intervention to 3/1,000 patient-days at risk post-intervention, but this difference did not reach statistical significance (P=0.08). Raman type 9 which belonged to ST239 was the single dominant MRSA clone. Conclusion The introduction of a bundle of preventive measures may reduce MRSA transmission and acquisition among surgery patients in a resource-limited hospital in Indonesia, but additional efforts are needed.
Collapse
Affiliation(s)
- Dewi Santosaningsih
- Department of Microbiology, Faculty of Medicine, Brawijaya University/Dr. Saiful Anwar Hospital, Malang, Indonesia.,Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Dewi Erikawati
- Department of Microbiology, Faculty of Medicine, Brawijaya University/Dr. Saiful Anwar Hospital, Malang, Indonesia
| | - Iffa A Hakim
- Department of Microbiology, Faculty of Medicine, Brawijaya University/Dr. Saiful Anwar Hospital, Malang, Indonesia
| | - Sanarto Santoso
- Department of Microbiology, Faculty of Medicine, Brawijaya University/Dr. Saiful Anwar Hospital, Malang, Indonesia
| | - M Hidayat
- Department of Orthopedic Surgery, Faculty of Medicine, Brawijaya University/Dr. Saiful Anwar Hospital, Malang, Indonesia
| | - Ayu H Suwenda
- Department of Orthopedic Surgery, Faculty of Medicine, Brawijaya University/Dr. Saiful Anwar Hospital, Malang, Indonesia
| | - Vicky Puspitasari
- Department of Pharmacy, Dr. Saiful Anwar Hospital, Malang, Indonesia
| | - Irhamni Irhamni
- Department of Pharmacy, Dr. Saiful Anwar Hospital, Malang, Indonesia
| | - Kuntaman Kuntaman
- Department of Microbiology, Faculty of Medicine, Airlangga University/Dr. Soetomo Hospital, Surabaya, Indonesia
| | - Andreas L E van Arkel
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Luke G Terlouw
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Neline Oudenes
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Diana Willemse-Erix
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Molecular Diagnostics, Jeroen Bosch Hospital, Tilburg, the Netherlands
| | - Susan V Snijders
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Nicole S Erler
- Department of Biostatistics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Henri A Verbrugh
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Juliëtte A Severin
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| |
Collapse
|
4
|
Niewiadomska AM, Jayabalasingham B, Seidman JC, Willem L, Grenfell B, Spiro D, Viboud C. Population-level mathematical modeling of antimicrobial resistance: a systematic review. BMC Med 2019; 17:81. [PMID: 31014341 PMCID: PMC6480522 DOI: 10.1186/s12916-019-1314-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/25/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Mathematical transmission models are increasingly used to guide public health interventions for infectious diseases, particularly in the context of emerging pathogens; however, the contribution of modeling to the growing issue of antimicrobial resistance (AMR) remains unclear. Here, we systematically evaluate publications on population-level transmission models of AMR over a recent period (2006-2016) to gauge the state of research and identify gaps warranting further work. METHODS We performed a systematic literature search of relevant databases to identify transmission studies of AMR in viral, bacterial, and parasitic disease systems. We analyzed the temporal, geographic, and subject matter trends, described the predominant medical and behavioral interventions studied, and identified central findings relating to key pathogens. RESULTS We identified 273 modeling studies; the majority of which (> 70%) focused on 5 infectious diseases (human immunodeficiency virus (HIV), influenza virus, Plasmodium falciparum (malaria), Mycobacterium tuberculosis (TB), and methicillin-resistant Staphylococcus aureus (MRSA)). AMR studies of influenza and nosocomial pathogens were mainly set in industrialized nations, while HIV, TB, and malaria studies were heavily skewed towards developing countries. The majority of articles focused on AMR exclusively in humans (89%), either in community (58%) or healthcare (27%) settings. Model systems were largely compartmental (76%) and deterministic (66%). Only 43% of models were calibrated against epidemiological data, and few were validated against out-of-sample datasets (14%). The interventions considered were primarily the impact of different drug regimens, hygiene and infection control measures, screening, and diagnostics, while few studies addressed de novo resistance, vaccination strategies, economic, or behavioral changes to reduce antibiotic use in humans and animals. CONCLUSIONS The AMR modeling literature concentrates on disease systems where resistance has been long-established, while few studies pro-actively address recent rise in resistance in new pathogens or explore upstream strategies to reduce overall antibiotic consumption. Notable gaps include research on emerging resistance in Enterobacteriaceae and Neisseria gonorrhoeae; AMR transmission at the animal-human interface, particularly in agricultural and veterinary settings; transmission between hospitals and the community; the role of environmental factors in AMR transmission; and the potential of vaccines to combat AMR.
Collapse
Affiliation(s)
- Anna Maria Niewiadomska
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, USA
| | - Bamini Jayabalasingham
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, USA.,Present Address: Elsevier Inc., 230 Park Ave, Suite B00, New York, NY, 10169, USA
| | - Jessica C Seidman
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, USA
| | | | - Bryan Grenfell
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, USA.,Princeton University, Princeton, NJ, USA
| | - David Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, USA.
| |
Collapse
|
5
|
Elshina E, Allen ER, Flaxman A, van Diemen PM, Milicic A, Rollier CS, Yamaguchi Y, Wyllie DH. Vaccination with the Staphylococcus aureus secreted proteins EapH1 and EapH2 impacts both S. aureus carriage and invasive disease. Vaccine 2018; 37:502-509. [PMID: 30502067 DOI: 10.1016/j.vaccine.2018.11.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 11/02/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022]
Abstract
INTRODUCTION There is a need for an efficacious vaccine reducing infections due to Staphylococcus aureus, a common cause of community and hospital infection. Infecting organisms originate from S. aureus populations colonising the nares and bowel. Antimicrobials are widely used to transiently reduce S. aureus colonisation prior to surgery, a practice which is selecting for resistant S. aureus isolates. S. aureus secretes multiple proteins, including the protease inhibitors extracellular adhesion protein homologue 1 and 2 (EapH1 and EapH2). METHODS Mice were vaccinated intramuscularly or intranasally with Adenovirus serotype 5 and Modified Vaccinia Ankara viral vectors expressing EapH1 and EapH2 proteins, or with control viruses. Using murine S. aureus colonisation models, we monitored S. aureus colonisation by sequential stool sampling. Monitoring of S. aureus invasive disease after intravenous challenge was performed using bacterial load and abscess numbers in the kidney. RESULTS Intramuscular vaccination with Adenovirus serotype 5 and Modified Vaccinia Ankara viral vectors expressing EapH1 and EapH2 proteins significantly reduces bacterial recovery in the murine renal abscess model of infection, but the magnitude of the effect is small. A single intranasal vaccination with an adenoviral vaccine expressing these proteins reduced S. aureus gastrointestinal (GI) tract colonisation. CONCLUSION Vaccination against EapH1 / EapH2 proteins may offer an antibiotic independent way to reduce S. aureus colonisation, as well as contributing to protection against S. aureus invasive disease.
Collapse
Affiliation(s)
- Elizaveta Elshina
- Jenner Institute, Centre for Cellular and Molecular Physiology, University of Oxford, United Kingdom
| | - Elizabeth R Allen
- Jenner Institute, Centre for Cellular and Molecular Physiology, University of Oxford, United Kingdom
| | - Amy Flaxman
- Jenner Institute, Centre for Cellular and Molecular Physiology, University of Oxford, United Kingdom
| | - Pauline M van Diemen
- Jenner Institute, Centre for Cellular and Molecular Physiology, University of Oxford, United Kingdom
| | - Anita Milicic
- Jenner Institute, Centre for Cellular and Molecular Physiology, University of Oxford, United Kingdom
| | - Christine S Rollier
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, United Kingdom
| | - Yuko Yamaguchi
- Jenner Institute, Centre for Cellular and Molecular Physiology, University of Oxford, United Kingdom
| | - David H Wyllie
- Jenner Institute, Centre for Cellular and Molecular Physiology, University of Oxford, United Kingdom.
| |
Collapse
|
6
|
Marbach H, Vizcay-Barrena G, Memarzadeh K, Otter JA, Pathak S, Allaker RP, Harvey RD, Edgeworth JD. Tolerance of MRSA ST239-TW to chlorhexidine-based decolonization: Evidence for keratinocyte invasion as a mechanism of biocide evasion. J Infect 2018; 78:119-126. [PMID: 30367885 DOI: 10.1016/j.jinf.2018.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/30/2018] [Accepted: 10/20/2018] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Information on genetic determinants of chlorhexidine tolerance (qacA carriage and MIC) in vitro is available, although evidence of the clinical impact and mechanisms remain poorly understood. We investigated why, following chlorhexidine intervention, prevalent epidemic MRSA ST22 and ST36 clones declined at an ICU, whilst an ST239-TW clone did not. The chlorhexidine tolerant ST239-TW phenotypes were assessed for their protein binding, cell adhesion and intracellular uptake potential. METHODS Six ST22, ST36 and ST239-TW bloodstream infection isolates with comparable chlorhexidine MICs were selected from a 2-year outbreak in an ICU at Guy's and St. Thomas' Hospital. Isolates were tested for fibrinogen and fibronectin binding, and adhesion/internalization into human keratinocytes with and without biocide. RESULTS Binding to fibrinogen and fibronectin, adhesion and intracellular uptake within keratinocytes (P < 0.001) and intracellular survival in keratinocytes under chlorhexidine pressure (ST22 3.18%, ST36 4.57% vs ST239-TW 12.79%; P < 0.0001) was consistently higher for ST239-TW. CONCLUSIONS We present evidence that MRSA clones with similarly low in vitro tolerance to chlorhexidine exhibit different in vivo susceptibilities. The phenomenon of S. aureus adhesion and intracellular uptake into keratinocytes could therefore be regarded as an additional mechanism of chlorhexidine tolerance, enabling MRSA to evade infection control measures.
Collapse
Affiliation(s)
- Helene Marbach
- Faculty of Life Sciences and Medicine, Institute of Pharmaceutical Science, King's College London, UK
| | - Gema Vizcay-Barrena
- Centre for Ultrastructural Imaging, King's College London, Guy's Campus, London, UK
| | - Kaveh Memarzadeh
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jonathan A Otter
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research (CIDR), King's College London & Guy's and St. Thomas' NHS Foundation Trust (GSTT), London, UK
| | - Smriti Pathak
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research (CIDR), King's College London & Guy's and St. Thomas' NHS Foundation Trust (GSTT), London, UK
| | - Robert P Allaker
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Richard D Harvey
- Faculty of Life Sciences and Medicine, Institute of Pharmaceutical Science, King's College London, UK.
| | - Jonathan D Edgeworth
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research (CIDR), King's College London & Guy's and St. Thomas' NHS Foundation Trust (GSTT), London, UK
| |
Collapse
|
7
|
Quantifying Hospital-Acquired Carriage of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae Among Patients in Dutch Hospitals. Infect Control Hosp Epidemiol 2017; 39:32-39. [DOI: 10.1017/ice.2017.241] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUNDExtended-spectrum β-lactamase–producing Enterobacteriaceae (ESBL-E) are emerging worldwide. Contact precautions are recommended for known ESBL-E carriers to control the spread of ESBL-E within hospitals.OBJECTIVEThis study quantified the acquisition of ESBL-E rectal carriage among patients in Dutch hospitals, given the application of contact precautions.METHODSData were used from 2 cluster-randomized studies on isolation strategies for ESBL-E: (1) the SoM study, performed in 14 Dutch hospitals from 2011 through 2014 and (2) the R-GNOSIS study, for which data were limited to those collected in a Dutch hospital in 2014. Perianal cultures were obtained, either during ward-based prevalence surveys (SoM), or at admission and twice weekly thereafter (R-GNOSIS). In both studies, contact precautions were applied to all known ESBL-E carriers. Estimates for acquisition of ESBL-E were based on the results of admission and discharge cultures from patients hospitalized for more than 2 days (both studies) and a Markov chain Monte Carlo (MCMC) model, applied to all patients hospitalized (R-GNOSIS).RESULTSThe absolute risk of acquisition of ESBL-E rectal carriage ranged from 2.4% to 2.9% with an ESBL-E acquisition rate of 2.8 to 3.8 acquisitions per 1,000 patient days. In addition, 28% of acquisitions were attributable to patient-dependent transmission, and the per-admission reproduction number was 0.06.CONCLUSIONSThe low ESBL-E acquisition rate in this study demonstrates that it is possible to control the nosocomial transmission of ESBL in a low-endemic, non-ICU setting whereEscherichia coliis the most prevalent ESBL-E and standard and contact precautions are applied for known ESBL-E carriers.TRIAL REGISTRATIONNederlands Trialregister, NTR2799,http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=2799; ISRCTN Registry, ISRCTN57648070,http://www.isrctn.com/ISRCTN57648070Infect Control Hosp Epidemiol2018;39:32–39
Collapse
|
8
|
Vali L, Dashti AA, Mathew F, Udo EE. Characterization of Heterogeneous MRSA and MSSA with Reduced Susceptibility to Chlorhexidine in Kuwaiti Hospitals. Front Microbiol 2017; 8:1359. [PMID: 28775716 PMCID: PMC5517409 DOI: 10.3389/fmicb.2017.01359] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 07/04/2017] [Indexed: 11/20/2022] Open
Abstract
The objective of this investigation was to identify the lineages of MRSA and MSSA with reduced susceptibility to chlorhexidine in Kuwaiti hospitals. 121 clinical MRSA and 56 MSSA isolates were included in this study. Antimicrobial susceptibility testing was performed for a selection of agents including chlorhexidine and resistance genes were amplified and sequenced. PFGE, spa typing, and MLST were completed for a selection of isolates. The results showed SCCmec II, III, IV, and V were present in 0.8, 21.5, 69.4, and 8.3% of the MRSA isolates. agr-1Sa was the most prevalent type in both MSSA (48%) and MRSA (54%). Forty-five percentage of MRSA contained pvl and 39% contained lukE-lukD, however, as many as 86% of MSSA contained pvl and 96.4% contained lukE-lukD. qac A-C genes were identified in 12.3% of MRSA, norA was present in 82.6% and blaZ in 94.2%. Among MSSA only 5.4% harbored qacA, 83% contained norA, and 91% blaZ. Multi-drug resistant ST239/t945 lineage containing a qac gene was the most identified S. aureus. However, other lineages, including ST772-MRSA-V/t4867/pvl(+)qacC/smr and non-qac harboring lineages of ST217-MRSAIV/t3244/pvl(-), ST34-MSSA/t161/pvl(+), ST5-MSSA/t688/pvl(+), ST5-MSSA/t4867/norA(+), and ST672-MSSA/t003/pvl(-), also showed reduced susceptibility to chlorhexidine. The observed reduced susceptibility of non-qac dependent MSSA isolates to chlorhexidine suggests the involvement of other elements in promoting higher MBC (≥30 mg/L). Our results confirm that monitoring MSSA is essential as they may have the potential to survive low level biocide exposure.
Collapse
Affiliation(s)
- Leila Vali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait UniversitySulaibekhat, Kuwait
| | - Ali A. Dashti
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait UniversitySulaibekhat, Kuwait
| | - Febine Mathew
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait UniversitySulaibekhat, Kuwait
| | - Edet E. Udo
- Department of Medical Microbiology, Faculty of Medicine, Kuwait UniversitySulaibekhat, Kuwait
| |
Collapse
|
9
|
Nübel U. Emergence and Spread of Antimicrobial Resistance: Recent Insights from Bacterial Population Genomics. Curr Top Microbiol Immunol 2017; 398:35-53. [PMID: 27738914 DOI: 10.1007/82_2016_505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Driven by progress of DNA sequencing technologies, recent population genomics studies have revealed that several bacterial pathogens constitute 'measurably evolving populations'. As a consequence, it was possible to reconstruct the emergence and spatial spread of drug-resistant bacteria on the basis of temporally structured samples of bacterial genome sequences. Based on currently available data, some general inferences can be drawn across different bacterial species as follows: (1) Resistance to various antibiotics evolved years to decades earlier than had been anticipated on the basis of epidemiological surveillance data alone. (2) Resistance traits are more rapidly acquired than lost and commonly persist in bacterial populations for decades. (3) Global populations of drug-resistant pathogens are dominated by very few clones, yet the features enabling such spreading success have not been revealed, aside from antibiotic resistance. (4) Whole-genome sequencing proved very effective at identifying bacterial isolates as parts of the same transmission networks.
Collapse
Affiliation(s)
- Ulrich Nübel
- DZIF Group on Microbial Genome Research, Leibniz Institute DSMZ, Braunschweig, Germany. .,Technical University Braunschweig, Braunschweig, Germany. .,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.
| |
Collapse
|
10
|
Cule M, Donnelly P. Stochastic modelling and inference in electronic hospital databases for the spread of infections: Clostridium difficile transmission in Oxfordshire hospitals 2007-2010. Ann Appl Stat 2017; 11:655-679. [PMID: 31105805 PMCID: PMC6520235 DOI: 10.1214/16-aoas1011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The combination of genetic information with electronic patient records promises to provide a powerful new resource for understanding human disease and its treatment. Here we develop and apply a novel stochastic compartmental model to a large dataset on Clostridium difficile infection (CDI) in three Oxfordshire hospitals over a 2.5 year period which combines genetic information on 858 confirmed cases of CDI with a database of 750,000 patient records. C. difficile is a major cause of healthcare-associated diarrhoea and is responsible for substantial mortality and morbidity, with relatively little known about its biology or its transmission epidemiology. Bayesian analysis of our model, via Markov chain Monte Carlo, provides new information about the biology of CDI, including genetic heterogeneity in infectiousness across different sequence types, and evidence for ward contamination as a significant mode of transmission, and allows inferences about the contribution of particular individuals, wards, or hospitals to transmission of the bacterium, and assessment of changes in these over time following changes in hospital practice. Our work demonstrates the value of using statistical modelling and computational inference on large-scale hospital patient databases and genetic data.
Collapse
Affiliation(s)
- Madeleine Cule
- Department of Statistics, 1 South Parks Road, Oxford OX1 3TG
| | - Peter Donnelly
- Department of Statistics, 1 South Parks Road, Oxford OX1 3TG
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN
| |
Collapse
|
11
|
Hetem DJ, Bootsma MCJ, Bonten MJM. Reply to Deeny et al. Clin Infect Dis 2016; 62:1194-5. [DOI: 10.1093/cid/ciw079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
12
|
Aryee A, Edgeworth JD. Carriage, Clinical Microbiology and Transmission of Staphylococcus aureus. Curr Top Microbiol Immunol 2016; 409:1-19. [PMID: 27097812 DOI: 10.1007/82_2016_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Staphylococcus aureus is one of the most important bacterial pathogens in clinical practice and a major diagnostic focus for the routine microbiology laboratory. It is carried as a harmless commensal in up to two-thirds of the population at any one time predominantly not only in the anterior nares, but also in multiple other sites such as the groin, axilla, throat, perineum, vagina and rectum. It colonizes skin breach sites, such as ulcers and wounds, and causes superficial and deep skin and soft tissue infections and life-threatening deep seated infections particularly endocarditis and osteomyelitis. S. aureus is constantly evolving through mutation and uptake of mobile genetic elements that confer increasing resistance and virulence. Since the 1960s, hospitals have had to contend with emergence of methicillin-resistant S. aureus (MRSA) strains that spread better in hospitals than methicillin-susceptible S. aureus (MSSA) and are harder to treat. Since the 1980s, distinct community MRSA strains have also emerged that cause severe skin and respiratory infections. Conventional identification of MSSA and MRSA in the microbiology laboratory involves microscopy, culture and biochemical analysis that for most samples is straightforward but slow, taking at least 48 h. This delay has significant consequences for individual patient care and public health, through inadequate or excessive empiric antibiotic use, and failure to implement appropriate infection control measures for MRSA-colonized patients during those first 48 h. This unmet need has driven development of rapid molecular diagnostics that either complement or replace conventional culture techniques in the laboratory, or can be placed in the clinical environment as point-of-care (POC) devices. These new technologies provide results to clinicians anything from within an hour to 24 h, depending on sample and clinical setting, and should transform management of patients with S. aureus and other bacterial diseases; however, uptake is often slow due to the disruptive effect of new technologies, costs of transition and uncertainty of the optimal solution given successive advances. More evidence of the health economic, clinical and antimicrobial resistance benefit will help support introduction of these new technologies. Finally, preventing MRSA transmission has been a priority for healthcare organizations for many years. There have been significant recent reductions in transmission following local and national campaigns to re-enforce basic and heightened infection control interventions such as universal hand hygiene, barrier nursing, decolonization and isolation of MRSA-colonized patients detected through routine culture or screening policies. Developments in whole genome sequencing are providing greater insight into reservoirs and routes of transmission that should help better target interventions to ensure sustainable control of endemic strains and to identify and prevent emergence of new strains.
Collapse
Affiliation(s)
- Anna Aryee
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Kings College London and Guy's and St. Thomas' NHS Foundation Trust, 5th Floor North Wing, Westminster Bridge Road, London, SE1 7EH, UK
| | - Jonathan D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Kings College London and Guy's and St. Thomas' NHS Foundation Trust, 5th Floor North Wing, Westminster Bridge Road, London, SE1 7EH, UK.
| |
Collapse
|
13
|
Determinants of the Final Size and Case Rate of Nosocomial Outbreaks. PLoS One 2015; 10:e0138216. [PMID: 26371880 PMCID: PMC4570781 DOI: 10.1371/journal.pone.0138216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 08/27/2015] [Indexed: 12/31/2022] Open
Abstract
Different nosocomial pathogen species have varying infectivity and durations of infectiousness, while the transmission route determines the contact rate between pathogens and susceptible patients. To determine if the pathogen species and transmission route affects the size and spread of outbreaks, we perform a meta-analysis that examines data from 933 outbreaks of hospital-acquired infection representing 14 pathogen species and 8 transmission routes. We find that the mean number of cases in an outbreak is best predicted by the pathogen species and the mean number of cases per day is best predicted by the species-transmission route combination. Our fitted model predicts the largest mean number of cases for Salmonella outbreaks (22.3) and the smallest mean number of cases for Streptococci outbreaks (8.5). The largest mean number of cases per day occurs during Salmonella outbreaks spread via the environment (0.33) and the smallest occurs for Legionella outbreaks spread by multiple transmission routes (0.005). When combined with information on the frequency of outbreaks these findings could inform the design of infection control policies in hospitals.
Collapse
|
14
|
Deeny SR, Worby CJ, Tosas Auguet O, Cooper BS, Edgeworth J, Cookson B, Robotham JV. Impact of mupirocin resistance on the transmission and control of healthcare-associated MRSA. J Antimicrob Chemother 2015; 70:3366-78. [PMID: 26338047 PMCID: PMC4652683 DOI: 10.1093/jac/dkv249] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/20/2015] [Indexed: 12/11/2022] Open
Abstract
Objectives The objectives of this study were to estimate the relative transmissibility of mupirocin-resistant (MupR) and mupirocin-susceptible (MupS) MRSA strains and evaluate the long-term impact of MupR on MRSA control policies. Methods Parameters describing MupR and MupS strains were estimated using Markov chain Monte Carlo methods applied to data from two London teaching hospitals. These estimates parameterized a model used to evaluate the long-term impact of MupR on three mupirocin usage policies: ‘clinical cases’, ‘screen and treat’ and ‘universal’. Strategies were assessed in terms of colonized and infected patient days and scenario and sensitivity analyses were performed. Results The transmission probability of a MupS strain was 2.16 (95% CI 1.38–2.94) times that of a MupR strain in the absence of mupirocin usage. The total prevalence of MupR in colonized and infected MRSA patients after 5 years of simulation was 9.1% (95% CI 8.7%–9.6%) with the ‘screen and treat’ mupirocin policy, increasing to 21.3% (95% CI 20.9%–21.7%) with ‘universal’ mupirocin use. The prevalence of MupR increased in 50%–75% of simulations with ‘universal’ usage and >10% of simulations with ‘screen and treat’ usage in scenarios where MupS had a higher transmission probability than MupR. Conclusions Our results provide evidence from a clinical setting of a fitness cost associated with MupR in MRSA strains. This provides a plausible explanation for the low levels of mupirocin resistance seen following ‘screen and treat’ mupirocin usage. From our simulations, even under conservative estimates of relative transmissibility, we see long-term increases in the prevalence of MupR given ‘universal’ use.
Collapse
Affiliation(s)
- Sarah R Deeny
- Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England and Health Protection Research Unit in Modelling Methodology, London, UK
| | - Colin J Worby
- Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA, USA
| | - Olga Tosas Auguet
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, King's College London, London, UK Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Ben S Cooper
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Jonathan Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, King's College London, London, UK Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Barry Cookson
- Division of Infection and Immunity, University College London, London, UK
| | - Julie V Robotham
- Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England and Health Protection Research Unit in Modelling Methodology, London, UK
| |
Collapse
|
15
|
Punina NV, Makridakis NM, Remnev MA, Topunov AF. Whole-genome sequencing targets drug-resistant bacterial infections. Hum Genomics 2015; 9:19. [PMID: 26243131 PMCID: PMC4525730 DOI: 10.1186/s40246-015-0037-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/03/2015] [Indexed: 01/07/2023] Open
Abstract
During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of Public Health, Epidemiology, Health Economics, and national productivity. Today’s WGS technologies are able to compete with conventional techniques in cost, speed, accuracy, and resolution for day-to-day control of infectious diseases and outbreaks in clinical laboratories and in long-term epidemiological investigations. WGS gives rise to an exciting future direction for personalized Genomic Epidemiology. One of the most vital and growing public health problems is the emerging and re-emerging of multidrug-resistant (MDR) bacterial infections in the communities and healthcare settings, reinforced by a decline in antimicrobial drug discovery. In recent years, retrospective analysis provided by WGS has had a great impact on the identification and tracking of MDR microorganisms in hospitals and communities. The obtained genomic data are also important for developing novel easy-to-use diagnostic assays for clinics, as well as for antibiotic and therapeutic development at both the personal and population levels. At present, this technology has been successfully applied as an addendum to the real-time diagnostic methods currently used in clinical laboratories. However, the significance of WGS for public health may increase if: (a) unified and user-friendly bioinformatics toolsets for easy data interpretation and management are established, and (b) standards for data validation and verification are developed. Herein, we review the current and future impact of this technology on diagnosis, prevention, treatment, and control of MDR infectious bacteria in clinics and on the global scale.
Collapse
Affiliation(s)
- N V Punina
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia.
| | - N M Makridakis
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - M A Remnev
- The Federal State Unitary Enterprise All-Russia Research Institute of Automatics, Moscow, 127055, Russia
| | - A F Topunov
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia
| |
Collapse
|
16
|
Interindividual Contacts and Carriage of Methicillin-Resistant Staphylococcus aureus: A Nested Case-Control Study. Infect Control Hosp Epidemiol 2015; 36:922-9. [PMID: 25892162 DOI: 10.1017/ice.2015.89] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Reducing the spread of multidrug-resistant bacteria in hospitals remains a challenge. Current methods are screening of patients, isolation, and adherence to hygiene measures among healthcare workers (HCWs). More specific measures could rely on a better characterization of the contacts at risk of dissemination. OBJECTIVE To quantify how close-proximity interactions (CPIs) affected Staphylococcus aureus dissemination. DESIGN Nested case-control study. SETTING French long-term care facility in 2009. PARTICIPANTS Patients (n=329) and HCWs (n=261). METHODS We recorded CPIs using electronic devices together with S. aureus nasal carriage during 4 months in all participants. Cases consisted of patients showing incident S. aureus colonization and were paired to 8 control patients who did not exhibit incident colonization at the same date. Conditional logistic regression was used to quantify associations between incidence and exposure to demographic, network, and carriage covariables. RESULTS The local structure of contacts informed on methicillin-resistant S. aureus (MRSA) carriage acquisition: CPIs with more HCWs were associated with incident MRSA colonization in patients (odds ratio [OR], 1.10 [95% CI, 1.04-1.17] for 1 more HCW), as well as longer CPI durations (1.03 [1.01-1.06] for a 1-hour increase). Joint analysis of carriage and contacts showed increased carriage acquisition in case of CPI with another colonized individual (OR, 1.55 [1.14-2.11] for 1 more HCW). Global network measurements did not capture associations between contacts and carriage. CONCLUSIONS Electronically recorded CPIs inform on the risk of MRSA carriage, warranting more study of in-hospital contact networks to design targeted intervention strategies.
Collapse
|
17
|
Update on linezolid in vitro activity through the Zyvox Annual Appraisal of Potency and Spectrum Program, 2013. Antimicrob Agents Chemother 2015; 59:2454-7. [PMID: 25645839 DOI: 10.1128/aac.04784-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Linezolid showed MIC50s and MIC90s of 1 μg/ml (for both) against Staphylococcus aureus. Two S. aureus strains exhibited higher MICs (4 to 8 μg/ml) caused by cfr and/or target site mutations, including the first detection of cfr in Poland. Linezolid (MIC50 and MIC90, 0.5 and 1 μg/ml) had potent MICs against coagulase-negative staphylococci (CoNS). Four CoNS had MICs of 16 to 128 μg/ml due to alterations in 23S rRNA and/or L3/L4. Linezolid inhibited all enterococci and streptococci at ≤2 μg/ml, except for one Enterococcus faecium strain (MIC, 8 μg/ml; G2576T [Escherichia coli numbering] mutation).
Collapse
|
18
|
Wyllie D, Davies J. Role of data warehousing in healthcare epidemiology. J Hosp Infect 2015; 89:267-70. [PMID: 25737091 DOI: 10.1016/j.jhin.2015.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 01/06/2015] [Indexed: 02/04/2023]
Abstract
Electronic storage of healthcare data, including individual-level risk factors for both infectious and other diseases, is increasing. These data can be integrated at hospital, regional and national levels. Data sources that contain risk factor and outcome information for a wide range of conditions offer the potential for efficient epidemiological analysis of multiple diseases. Opportunities may also arise for monitoring healthcare processes. Integrating diverse data sources presents epidemiological, practical, and ethical challenges. For example, diagnostic criteria, outcome definitions, and ascertainment methods may differ across the data sources. Data volumes may be very large, requiring sophisticated computing technology. Given the large populations involved, perhaps the most challenging aspect is how informed consent can be obtained for the development of integrated databases, particularly when it is not easy to demonstrate their potential. In this article, we discuss some of the ups and downs of recent projects as well as the potential of data warehousing for antimicrobial resistance monitoring.
Collapse
Affiliation(s)
- D Wyllie
- Public Health England Academic Collaborating Centre, John Radcliffe Hospital, Oxford, UK.
| | - J Davies
- Oxford NIHR BRC Informatics Programme, Department of Computer Science, University of Oxford, Oxford, UK
| |
Collapse
|
19
|
Tong SYC, Holden MTG, Nickerson EK, Cooper BS, Köser CU, Cori A, Jombart T, Cauchemez S, Fraser C, Wuthiekanun V, Thaipadungpanit J, Hongsuwan M, Day NP, Limmathurotsakul D, Parkhill J, Peacock SJ. Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting. Genome Res 2014; 25:111-8. [PMID: 25491771 PMCID: PMC4317166 DOI: 10.1101/gr.174730.114] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infection. Whole-genome sequencing of MRSA has been used to define phylogeny and transmission in well-resourced healthcare settings, yet the greatest burden of nosocomial infection occurs in resource-restricted settings where barriers to transmission are lower. Here, we study the flux and genetic diversity of MRSA on ward and individual patient levels in a hospital where transmission was common. We repeatedly screened all patients on two intensive care units for MRSA carriage over a 3-mo period. All MRSA belonged to multilocus sequence type 239 (ST 239). We defined the population structure and charted the spread of MRSA by sequencing 79 isolates from 46 patients and five members of staff, including the first MRSA-positive screen isolates and up to two repeat isolates where available. Phylogenetic analysis identified a flux of distinct ST 239 clades over time in each intensive care unit. In total, five main clades were identified, which varied in the carriage of plasmids encoding antiseptic and antimicrobial resistance determinants. Sequence data confirmed intra- and interwards transmission events and identified individual patients who were colonized by more than one clade. One patient on each unit was the source of numerous transmission events, and deep sampling of one of these cases demonstrated colonization with a "cloud" of related MRSA variants. The application of whole-genome sequencing and analysis provides novel insights into the transmission of MRSA in under-resourced healthcare settings and has relevance to wider global health.
Collapse
Affiliation(s)
- Steven Y C Tong
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom; Menzies School of Health Research, Darwin, Northern Territory 0811, Australia
| | - Matthew T G Holden
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Emma K Nickerson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom
| | - Ben S Cooper
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Claudio U Köser
- Department of Medicine, University of Cambridge, Cambridge CB2 OXY, United Kingdom; Public Health England, Cambridge CB2 0QW, United Kingdom
| | - Anne Cori
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, United Kingdom
| | - Thibaut Jombart
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, United Kingdom
| | - Simon Cauchemez
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, United Kingdom
| | - Christophe Fraser
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, United Kingdom
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Janjira Thaipadungpanit
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Maliwan Hongsuwan
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Nicholas P Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sharon J Peacock
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom; Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; Department of Medicine, University of Cambridge, Cambridge CB2 OXY, United Kingdom; Public Health England, Cambridge CB2 0QW, United Kingdom
| |
Collapse
|
20
|
Empfehlungen zur Prävention und Kontrolle von Methicillin-resistenten Staphylococcus aureus-Stämmen (MRSA) in medizinischen und pflegerischen Einrichtungen. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2014. [DOI: 10.1007/s00103-014-1980-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
21
|
Santosaningsih D, Santoso S, Budayanti NS, Kuntaman K, Lestari ES, Farida H, Hapsari R, Hadi P, Winarto W, Milheiriço C, Maquelin K, Willemse-Erix D, van Belkum A, Severin JA, Verbrugh HA. Epidemiology of Staphylococcus aureus harboring the mecA or Panton-Valentine leukocidin genes in hospitals in Java and Bali, Indonesia. Am J Trop Med Hyg 2014; 90:728-34. [PMID: 24567320 DOI: 10.4269/ajtmh.13-0734] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Data of Staphylococcus aureus carriage in Indonesian hospitals are scarce. Therefore, the epidemiology of S. aureus among surgery patients in three academic hospitals in Indonesia was studied. In total, 366 of 1,502 (24.4%) patients carried S. aureus. The methicillin-resistant S. aureus (MRSA) carriage rate was 4.3%, whereas 1.5% of the patients carried Panton-Valentine leukocidin (PVL)-positive methicillin-sensitive S. aureus (MSSA). Semarang and Malang city (odds ratio [OR] 9.4 and OR 9.0), being male (OR 2.4), hospitalization for more than 5 days (OR 11.708), and antibiotic therapy during hospitalization (OR 2.6) were independent determinants for MRSA carriage, whereas prior hospitalization (OR 2.5) was the only one risk factor for PVL-positive MSSA carriage. Typing of MRSA strains by Raman spectroscopy showed three large clusters assigned type 21, 24, and 38, all corresponding to ST239-MRSA-SCCmec type III. In conclusion, MRSA and PVL-positive MSSA are present among patients in surgical wards in Indonesian academic hospitals.
Collapse
Affiliation(s)
- Dewi Santosaningsih
- Department of Microbiology, Faculty of Medicine, Brawijaya University/Dr. Saiful Anwar Hospital, Malang, Indonesia; Department of Microbiology, Faculty of Medicine, Udayana University/Sanglah Hospital, Denpasar, Bali, Indonesia; Department of Microbiology, Faculty of Medicine, Airlangga University/Dr. Soetomo Hospital, Surabaya, Indonesia; Department of Microbiology, Faculty of Medicine, Diponegoro University/Dr. Kariadi Hospital, Semarang, Indonesia; Laboratory of Molecular Genetics, Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal; Center for Optical Diagnostics and Therapy, Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Lee AS, Cooper BS, Malhotra-Kumar S, Chalfine A, Daikos GL, Fankhauser C, Carevic B, Lemmen S, Martínez JA, Masuet-Aumatell C, Pan A, Phillips G, Rubinovitch B, Goossens H, Brun-Buisson C, Harbarth S. Comparison of strategies to reduce meticillin-resistant Staphylococcus aureus rates in surgical patients: a controlled multicentre intervention trial. BMJ Open 2013; 3:e003126. [PMID: 24056477 PMCID: PMC3780302 DOI: 10.1136/bmjopen-2013-003126] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To compare the effect of two strategies (enhanced hand hygiene vs meticillin-resistant Staphylococcus aureus (MRSA) screening and decolonisation) alone and in combination on MRSA rates in surgical wards. DESIGN Prospective, controlled, interventional cohort study, with 6-month baseline, 12-month intervention and 6-month washout phases. SETTING 33 surgical wards of 10 hospitals in nine countries in Europe and Israel. PARTICIPANTS All patients admitted to the enrolled wards for more than 24 h. INTERVENTIONS The two strategies compared were (1) enhanced hand hygiene promotion and (2) universal MRSA screening with contact precautions and decolonisation (intranasal mupirocin and chlorhexidine bathing) of MRSA carriers. Four hospitals were assigned to each intervention and two hospitals combined both strategies, using targeted MRSA screening. OUTCOME MEASURES Monthly rates of MRSA clinical cultures per 100 susceptible patients (primary outcome) and MRSA infections per 100 admissions (secondary outcome). Planned subgroup analysis for clean surgery wards was performed. RESULTS After adjusting for clustering and potential confounders, neither strategy when used alone was associated with significant changes in MRSA rates. Combining both strategies was associated with a reduction in the rate of MRSA clinical cultures of 12% per month (adjusted incidence rate ratios (aIRR) 0.88, 95% CI 0.79 to 0.98). In clean surgery wards, strategy 2 (MRSA screening, contact precautions and decolonisation) was associated with decreasing rates of MRSA clinical cultures (15% monthly decrease, aIRR 0.85, 95% CI 0.74 to 0.97) and MRSA infections (17% monthly decrease, aIRR 0.83, 95% CI 0.69 to 0.99). CONCLUSIONS In surgical wards with relatively low MRSA prevalence, a combination of enhanced standard and MRSA-specific infection control approaches was required to reduce MRSA rates. Implementation of single interventions was not effective, except in clean surgery wards where MRSA screening coupled with contact precautions and decolonisation was associated with significant reductions in MRSA clinical culture and infection rates. TRIAL REGISTRATION clinicaltrials.gov identifier: NCT00685867.
Collapse
Affiliation(s)
- Andie S Lee
- Infection Control Program, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
- Departments of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Ben S Cooper
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Nuffield Department of Clinical Medicine, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Surbhi Malhotra-Kumar
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Annie Chalfine
- Infection Control Unit, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - George L Daikos
- First Department of Propaedeutic Medicine, Laiko General Hospital, Athens, Greece
| | - Carolina Fankhauser
- Infection Control Program, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Biljana Carevic
- Department of Hospital Epidemiology, Clinical Center of Serbia, Belgrade, Serbia
| | - Sebastian Lemmen
- Department of Infection Control and Infectious Diseases, Universitätsklinikum Aachen, Aachen, Germany
| | | | - Cristina Masuet-Aumatell
- Preventive Medicine Department and Faculty of Medicine, Bellvitge Biomedical Research Institute (IDIBELL), University Hospital of Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Angelo Pan
- Infectious and Tropical Diseases Unit, Istituti Ospitalieri di Cremona, Cremona, Italy
| | - Gabby Phillips
- Infection Control Department, Ninewells Hospital, Dundee, Scotland
| | - Bina Rubinovitch
- Unit of Infection Control, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel
| | - Herman Goossens
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Christian Brun-Buisson
- Inserm U 657, Institut Pasteur, Paris; Department of Intensive Care, Hopital Henri Mondor, Universite Paris-Est Creteil, Creteil, France
| | - Stephan Harbarth
- Infection Control Program, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | | |
Collapse
|
23
|
Case and partnership reproduction numbers for a curable sexually transmitted infection. J Theor Biol 2013; 331:38-47. [DOI: 10.1016/j.jtbi.2013.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 11/18/2022]
|
24
|
Otter JA, Patel A, Cliff PR, Halligan EP, Tosas O, Edgeworth JD. Selection for qacA carriage in CC22, but not CC30, methicillin-resistant Staphylococcus aureus bloodstream infection isolates during a successful institutional infection control programme. J Antimicrob Chemother 2013; 68:992-9. [PMID: 23288405 DOI: 10.1093/jac/dks500] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The increasing use of chlorhexidine for methicillin-resistant Staphylococcus aureus (MRSA) decolonization raises concerns about reduced susceptibility. We evaluated the carriage of chlorhexidine resistance genes and chlorhexidine susceptibility in MRSA before and after introduction of an institutional MRSA control programme incorporating chlorhexidine-based decolonization in 2004. METHODS MRSA bloodstream infection (BSI) isolates identified between 2001 and 2009 were tested for spa and staphylococcal cassette chromosome mec type and carriage of qacA, qacB and smr. Selected isolates were tested for chlorhexidine susceptibility. Logistic regression was used to evaluate associations between clone type, carriage of resistance genes and chlorhexidine susceptibility. Temporal trends in qacA or smr carriage were analysed using separate binomial generalized linear models. RESULTS Typing identified two dominant clones: CC22 (n = 224) and CC30 (n = 197). Annual MRSA BSI rates declined from 2004, although the rate of decline for CC22 was slower than for CC30. Carriage of qacA and smr and having a chlorhexidine MIC ≥2 mg/L did not increase overall amongst MRSA BSI isolates; however, qacA carriage increased in CC22 compared with in CC30 (OR, 7.21; 95% CI, 1.32-39.17). Furthermore, qacA+ CC22 isolates were more likely to have a chlorhexidine MIC ≥2 mg/L than qacA+ CC30 isolates (OR, 21.67; CI, 2.54-185.20). CONCLUSIONS A successful infection control programme was associated with the selection of qacA linked with a higher chlorhexidine MIC in one dominant endemic MRSA clone (CC22), but not another (CC30). The slower reduction in the CC22 MRSA BSI rate suggests that carriage of qacA confers a selective advantage, with implications for the sustainability of decolonization practice.
Collapse
Affiliation(s)
- Jonathan A Otter
- Centre for Clinical Infection and Diagnostics Research (CIDR), Department of Infectious Diseases, King's College London & Guy's and St Thomas' NHS Foundation Trust, London, UK.
| | | | | | | | | | | |
Collapse
|