1
|
Genovese C, La Fauci V, D'Amato S, Squeri A, Anzalone C, Costa GB, Fedele F, Squeri R. Molecular epidemiology of antimicrobial resistant microorganisms in the 21th century: a review of the literature. ACTA BIO-MEDICA : ATENEI PARMENSIS 2020; 91:256-273. [PMID: 32420962 PMCID: PMC7569612 DOI: 10.23750/abm.v91i2.9176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/10/2020] [Indexed: 12/26/2022]
Abstract
Healthcare-associated infections (HAIs) are the most frequent and severe complication acquired in healthcare settings with high impact in terms of morbidity, mortality and costs. Many bacteria could be implicated in these infections, but, expecially multidrug resistance bacteria could play an important role. Many microbial typing technologies have been developed until to the the bacterial whole-genome sequencing and the choice of a molecular typing method therefore will depend on the skill level and resources of the laboratory and the aim and scale of the investigation. In several studies the molecular investigation of pathogens involved in HAIs was performed with many microorganisms identified as causative agents such as Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Clostridium difficile, Acinetobacter spp., Enterobacter spp., Enterococcus spp., Staphylococcus aureus and several more minor species. Here, we will describe the most and least frequently reported clonal complex, sequence types and ribotypes with their worldwide geographic distribution for the most important species involved in HAIs.
Collapse
Affiliation(s)
- Cristina Genovese
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Vincenza La Fauci
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Smeralda D'Amato
- Postgraduate Medical School in Hygiene and Preventive Medicine, University of Messina, Italy.
| | - Andrea Squeri
- Department of Human Pathology of the adult and developmental age Gaetano Barresi, University of Messina, Messina, Italy.
| | - Carmelina Anzalone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Gaetano Bruno Costa
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Francesco Fedele
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | | |
Collapse
|
2
|
Toleman MS, Watkins ER, Williams T, Blane B, Sadler B, Harrison EM, Coll F, Parkhill J, Nazareth B, Brown NM, Peacock SJ. Investigation of a Cluster of Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Transmission in a Community Setting. Clin Infect Dis 2017; 65:2069-2077. [PMID: 29077854 PMCID: PMC5850418 DOI: 10.1093/cid/cix539] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) has typically been used to confirm or refute hospital/ward outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) identified through routine practice. However, appropriately targeted WGS strategies that identify routinely "undetectable" transmission remain the ultimate aim. METHODS WGS of MRSA isolates sent to a regional microbiological laboratory was performed as part of a 12-month prospective observational study. Phylogenetic analyses identified a genetically related cluster of E-MRSA15 isolated from patients registered to the same general practice (GP) surgery. This led to an investigation to identify epidemiological links, find additional cases, and determine potential for ongoing transmission. RESULTS We identified 15 MRSA-positive individuals with 27 highly related MRSA isolates who were linked to the GP surgery, 2 of whom died with MRSA bacteremia. Of the 13 cases that were further investigated, 11 had attended a leg ulcer/podiatry clinic. Cases lacked epidemiological links to hospitals, suggesting that transmission occurred elsewhere. Environmental and staff screening at the GP surgery did not identify an ongoing source of infection. CONCLUSIONS Surveillance in the United Kingdom shows that the proportion of MRSA bacteremias apportioned to hospitals is decreasing, suggesting the need for greater focus on the detection of MRSA outbreaks and transmission in the community. This case study confirms that the typically nosocomial lineage (E-MRSA15) can transmit within community settings. Our study exemplifies the continued importance of WGS in detecting outbreaks, including those which may be missed by routine practice, and suggests that universal WGS of bacteremia isolates may help detect outbreaks in low-surveillance settings.
Collapse
Affiliation(s)
- Michelle S Toleman
- University of Cambridge
- Wellcome Trust Sanger Institute, Hinxton
- Cambridge University Hospitals NHS Foundation Trust
| | | | | | | | - Belinda Sadler
- Infection Prevention and Control, Cambridgeshire and Peterborough Clinical Commissioning Group
| | | | | | | | | | - Nicholas M Brown
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom
| | - Sharon J Peacock
- University of Cambridge
- Wellcome Trust Sanger Institute, Hinxton
- Cambridge University Hospitals NHS Foundation Trust
- London School of Hygiene and Tropical Medicine
| |
Collapse
|
3
|
Valle DL, Paclibare PAP, Cabrera EC, Rivera WL. Molecular and phenotypic characterization of methicillin-resistant Staphylococcus aureus isolates from a tertiary hospital in the Philippines. Trop Med Health 2016; 44:3. [PMID: 27398062 PMCID: PMC4934148 DOI: 10.1186/s41182-016-0003-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/15/2016] [Indexed: 11/10/2022] Open
Abstract
Background Methicillin-resistant Staphylococcus aureus (MRSA) poses a major threat to public health worldwide. There are relatively few studies addressing the molecular epidemiology of MRSA in the Philippines. Methods This study characterized MRSA isolates in terms of their antimicrobial susceptibility profile, the SCCmec type, and the presence of lukF-lukS genes for Panton-Valentine leukocidin (PVL) and determined the relatedness of the isolates by random amplified polymorphic DNA (RAPD)-polymerase chain reaction (PCR). Results A total of 236 S. aureus were isolated from clinical specimens of the Makati Medical Center in Makati City, Philippines, between January 2013 and June 2013, and 108 or 45.76 % were found to be MRSA. Results showed that the MRSA strains were resistant to trimethoprim-sulfamethoxazole (20.37 %), azithromycin (10.19 %), gentamicin (5.56 %), and linezolid (4.63 %), while all were susceptible to vancomycin, nitrofurantoin, levofloxacin, minocycline, rifampin, and tetracycline. One isolate was found positive for inducible clindamycin resistance. All of the 108 MRSA strains were confirmed to carry the mecA and SCCmec genes, while the PVL genes were detected in 41 (38 %) of the isolates. Ninety-six isolates (89 %) carried SCCmec type IV, while the remaining isolates carried SCCmec type I (11 isolates) or type III (one isolate). Conclusion This study is the first to present a comprehensive MRSA surveillance data with molecular characterization in a tertiary hospital in the Philippines.
Collapse
Affiliation(s)
- Demetrio L Valle
- Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, 1101 Philippines ; Department of Pathology and Laboratories, Makati Medical Center, Makati City, 1229 Philippines
| | - Phyllis Anne P Paclibare
- Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, 1101 Philippines ; Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101 Philippines
| | - Esperanza C Cabrera
- Biology Department, De La Salle University, Taft Ave., Manila City, 1004 Philippines
| | - Windell L Rivera
- Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, 1101 Philippines ; Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101 Philippines
| |
Collapse
|
4
|
Davis MF, Peterson AE, Julian KG, Greene WH, Price LB, Nelson K, Whitener CJ, Silbergeld EK. Household risk factors for colonization with multidrug-resistant Staphylococcus aureus isolates. PLoS One 2013; 8:e54733. [PMID: 23359808 PMCID: PMC3554652 DOI: 10.1371/journal.pone.0054733] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 12/14/2012] [Indexed: 12/22/2022] Open
Abstract
Antimicrobial resistance, particularly in pathogens such as methicillin-resistant Staphylococcus aureus (MRSA), limits treatment options and increases healthcare costs. To understand patient risk factors, including household and animal contact, potentially associated with colonization with multidrug-resistant MRSA isolates, we performed a prospective study of case patients colonized with MRSA on admission to a rural tertiary care hospital. Patients were interviewed and antimicrobial resistance patterns were tested among isolates from admitted patients colonized with MRSA in 2009-10. Prevalence of resistance was compared by case-patient risk factors and length-of-stay outcome among 88 MRSA case patients. Results were compared to NHANES 2003-04. Overall prevalence of multidrug resistance (non-susceptibility to ≥ four antimicrobial classes) in MRSA nasal isolates was high (73%) and was associated with a 1.5-day increase in subsequent length of stay (p = 0.008). History of hospitalization within the past six months, but not antimicrobial use in the same time period, was associated with resistance patterns. Within a subset of working-age case patients without recent history of hospitalization, animal contact was potentially associated with multidrug resistance. History of hospitalization, older age, and small household size were associated with multidrug resistance in NHANES data. In conclusion, recent hospitalization of case patients was predictive of antimicrobial resistance in MRSA isolates, but novel risk factors associated with the household may be emerging in CA-MRSA case patients. Understanding drivers of antimicrobial resistance in MRSA isolates is important to hospital infection control efforts, relevant to patient outcomes and to indicators of the economic burden of antimicrobial resistance.
Collapse
Affiliation(s)
- Meghan F Davis
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Peterson AE, Davis MF, Julian KG, Awantang G, Greene WH, Price LB, Waters A, Doppalapudi A, Krain LJ, Nelson K, Silbergeld EK, Whitener CJ. Molecular and phenotypic characteristics of healthcare- and community-associated methicillin-resistant Staphylococcus aureus at a rural hospital. PLoS One 2012; 7:e38354. [PMID: 22719880 PMCID: PMC3376098 DOI: 10.1371/journal.pone.0038354] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 05/07/2012] [Indexed: 01/03/2023] Open
Abstract
Background While methicillin-resistant Staphylococcus aureus (MRSA) originally was associated with healthcare, distinct strains later emerged in patients with no prior hospital contact. The epidemiology of MRSA continues to evolve. Methods To characterize the current epidemiology of MRSA-colonized patients entering a hospital serving both rural and urban communities, we interviewed patients with MRSA-positive admission nasal swabs between August 2009 and March 2010. We applied hospitalization risk factor, antimicrobial resistance phenotype, and multi-locus sequence genotype (MLST) classification schemes to 94 case-patients. Results By MLST analysis, we identified 15 strains with two dominant clonal complexes (CCs)–CC5 (51 isolates), historically associated with hospitals, and CC8 (27 isolates), historically of community origin. Among patients with CC5 isolates, 43% reported no history of hospitalization within the past six months; for CC8, 67% reported the same. Classification by hospitalization risk factor did not correlate strongly with genotypic classification. Sensitivity of isolates to ciprofloxacin, clindamycin, or amikacin was associated with the CC8 genotype; however, among CC8 strains, 59% were resistant to ciprofloxacin, 15% to clindamycin, and 15% to amikacin. Conclusions Hospitalization history was not a strong surrogate for the CC5 genotype. Conversely, patients with a history of hospitalization were identified with the CC8 genotype. Although ciprofloxacin, clindamycin, and amikacin susceptibility distinguished CC8 strains, the high prevalence of ciprofloxacin resistance limited its predictive value. As CC8 strains become established in healthcare settings and CC5 strains disseminate into the community, community-associated MRSA definitions based on case-patient hospitalization history may prove less valuable in tracking community MRSA strains.
Collapse
Affiliation(s)
- Amy E. Peterson
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Meghan F. Davis
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
| | - Kathleen G. Julian
- Penn State Hershey Medical Center, Hershey, Pennsylvania, United States of America
| | - Grace Awantang
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Wallace H. Greene
- Penn State Hershey Medical Center, Hershey, Pennsylvania, United States of America
| | - Lance B. Price
- The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Andrew Waters
- The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Avanthi Doppalapudi
- Penn State Hershey Medical Center, Hershey, Pennsylvania, United States of America
| | - Lisa J. Krain
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Kenrad Nelson
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Ellen K. Silbergeld
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Cynthia J. Whitener
- Penn State Hershey Medical Center, Hershey, Pennsylvania, United States of America
| |
Collapse
|
6
|
Wyllie DH, Walker AS, Miller R, Moore C, Williamson SR, Schlackow I, Finney JM, O'Connor L, Peto TEA, Crook DW. Decline of meticillin-resistant Staphylococcus aureus in Oxfordshire hospitals is strain-specific and preceded infection-control intensification. BMJ Open 2011; 1:e000160. [PMID: 22021779 PMCID: PMC3191576 DOI: 10.1136/bmjopen-2011-000160] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background In the past, strains of Staphylococcus aureus have evolved, expanded, made a marked clinical impact and then disappeared over several years. Faced with rising meticillin-resistant S aureus (MRSA) rates, UK government-supported infection control interventions were rolled out in Oxford Radcliffe Hospitals NHS Trust from 2006 onwards. Methods Using an electronic Database, the authors identified isolation of MRS among 611 434 hospital inpatients admitted to acute hospitals in Oxford, UK, 1 April 1998 to 30 June 2010. Isolation rates were modelled using segmented negative binomial regression for three groups of isolates: from blood cultures, from samples suggesting invasion (eg, cerebrospinal fluid, joint fluid, pus samples) and from surface swabs (eg, from wounds). Findings MRSA isolation rates rose rapidly from 1998 to the end of 2003 (annual increase from blood cultures 23%, 95% CI 16% to 30%), and then declined. The decline accelerated from mid-2006 onwards (annual decrease post-2006 38% from blood cultures, 95% CI 29% to 45%, p=0.003 vs previous decline). Rates of meticillin-sensitive S aureus changed little by comparison, with no evidence for declines 2006 onward (p=0.40); by 2010, sensitive S aureus was far more common than MRSA (blood cultures: 2.9 vs 0.25; invasive samples 14.7 vs 2.0 per 10 000 bedstays). Interestingly, trends in isolation of erythromycin-sensitive and resistant MRSA differed. Erythromycin-sensitive strains rose significantly faster (eg, from blood cultures p=0.002), and declined significantly more slowly (p=0.002), than erythromycin-resistant strains (global p<0.0001). Bacterial typing suggests this reflects differential spread of two major UK MRSA strains (ST22/36), ST36 having declined markedly 2006-2010, with ST22 becoming the dominant MRSA strain. Conclusions MRSA isolation rates were falling before recent intensification of infection-control measures. This, together with strain-specific changes in MRSA isolation, strongly suggests that incompletely understood biological factors are responsible for the much recent variation in MRSA isolation. A major, mainly meticillin-sensitive, S aureus burden remains.
Collapse
Affiliation(s)
- David H Wyllie
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - A Sarah Walker
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- MRC Clinical Trials Unit, London, UK
| | - Ruth Miller
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Catrin Moore
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | | | - Iryna Schlackow
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - John M Finney
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Lily O'Connor
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Tim E A Peto
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Derrick W Crook
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| |
Collapse
|