Comparison of pulsed-gel electrophoresis and a commercial repetitive-element PCR method for assessment of methicillin-resistant Staphylococcus aureus clustering in different health care facilities

Differentiation of Community-Associated and Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolates and Identification of spa Types by Use of PCR and High-Resolution Melt Curve Analysis

Infections due to methicillin-resistant Staphylococcus aureus (MRSA) are present worldwide and represent a major public health concern. The capability of PCR followed by high-resolution melt (HRM) curve analysis for the detection of community-associated and livestock-associated MRSA strains and the identification of staphylococcal protein A (spa) locus was evaluated in 74 MRSA samples which were isolated from the environment, humans, and pigs on a single piggery. PCR-HRM curve analysis identified four spa types among MRSA samples and differentiated MRSA strains accordingly. A nonsubjective differentiation model was developed according to genetic confidence percentage values produced by tested samples, which did not require visual interpretation of HRM curve results. The test was carried out at different settings, and result data were reanalyzed and confirmed with DNA sequencing. PCR-HRM curve analysis proved to be a robust and reliable test for spa typing and can be used as a tool in epidemiological studies.

Genotypic and phenotypic characterization of Salmonella enterica subsp. enterica serovar Typhimurium monophasic variants isolated in Thailand and Japan

Monophasic variants of Salmonella enterica serovar Typhimurium isolated in Thailand and Japan were characterized to elucidate the genetic basis of the monophasic phenotype, genetic relatedness, and antimicrobial resistance. A total of 20 Salmonella isolates agglutinated with anti-O4 and anti-H:i serum and not agglutinated with either anti-H:1 or anti-H:2 serum were identified as monophasic variants of Salmonella serovar Typhimurium because they harbored IS200, specific to this serovar, and lacked the fljB gene. An allele-specific PCR-based genotyping method that detects a clade-specific single nucleotide polymorphism indicated that seven swine isolates and one human isolate from Thailand were grouped into clade 1; five isolates from layer chicken houses and layer chicken feces from Japan were grouped into clade 8, together with two Salmonella serovar Typhimurium isolates from chicken houses in Japan; and five isolates from swine feces from Thailand and two isolates from layer chicken feces from Japan were grouped into clade 9. Multilocus sequencing typing demonstrated that sequence type (ST) 34 isolates were solely grouped into clade 9. Clade 1 and 8 isolates were assigned as ST19. Pulsed-field gel electrophoresis revealed multiple types within each of the clades. The presence of antimicrobial resistance genes and plasmid replicon type, of the clade 1 and 9 isolates were comparable to those reported for epidemic strains of monophasic variants. Our results suggest that monitoring monophasic variants of serovar Typhimurium is important for understanding of the spread of these variants in Thailand and Japan.

Measuring radiation-induced DNA damage in Cryptococcus neoformans and Saccharomyces cerevisiae using long range quantitative PCR

DNA damage has been considered to be the universal critical lesion in cells after exposure to ionizing radiation. Measuring radiation-induced DNA damage is important to understand the mechanisms of radiation-induced toxicity and monitor DNA damage repairs. Currently the most widely used methods to measure DNA damage are pulsed-field gel electrophoresis (PFGF) and single-cell gel electrophoresis (also known as the comet assay), both of which are technically challenging and time consuming. Long range quantitative polymerase chain reaction (LR-QPCR) has been used successfully to measure nuclear and mitochondrial DNA damage in mammalian and several model organism cells. The principle of this assay is that DNA lesions will slow down or block the progression of DNA polymerase. Therefore, the amplification efficiency of DNA with fewer lesions will be higher than DNA with more lesions under the same reaction condition. Here, we developed the LR-QPCR assay primers and reaction conditions to quantify DNA damage in Cryptococcus neoformans (C. neoformans) and Saccharomyces cerevisiae (S. cerevisiae) after gamma ray exposure. Under these conditions, long DNA targets of C. neoformans H99 and S. cerevisiae BY4741 (17.6 and 16.4 kb for nuclear DNA and 15.3 and 14.6 kb for mitochondrial DNA) were quantitatively amplified using extracted DNA templates, respectively. Two short mitochondrial DNA targets of these two species (207 bp and 154 bp) were also quantitatively amplified and used to monitor the number of mitochondria. Using the LR-QPCR method, we showed that the frequency of radiation-induced mitochondrial and nuclear DNA lesions had a significant linear correlation with the radiation doses (from 500 Gy to 3000 Gy) in both species. Furthermore, the faster disappearance of DNA damage detected in C. neoformans H99S strain compared to H99 strain may help to explain the different radiation sensitivity of these two strains. In summary, we developed a simple, sensitive method to measure radiation-induced DNA damage, which can greatly facilitate the study of radiation-induced toxicity and can be widely used as a dosimetry in radiation-induced cell damage.

How to: molecular investigation of a hospital outbreak

BACKGROUND

Studying hospital outbreaks by using molecular tools, i.e. synthesizing the molecular epidemiology data to its appropriate clinical-epidemiologic context, is crucial in order to identify infection source, infer transmission dynamics, appropriately allocate prevention resources and implement control measures. Whole-genome sequencing (WGS) of pathogens has become the reference standard, as it is becoming more accessible and affordable. Consequently, sequencing of the full pathogen genome via WGS and major progress in fit-for-purpose genomic data analysis tools and interpretation is revolutionizing the field of outbreak investigations in hospitals. Metagenomics is an additional evolving field that might become commonly used in the future for outbreak investigations. Nevertheless, practitioners are frequently limited in terms of WGS or metagenomics, especially for local outbreak analyses, as a result of costs or logistical considerations, reduced or lack of locally available resources and/or expertise. As a result, traditional approaches, including pulsed-field gel electrophoresis, repetitive-element palindromic PCR and multilocus sequence typing, along with other typing methods, are still widely used.

AIMS

To provide practitioners with evidenced-based action plans for usage of the various typing techniques in order to investigate the molecular epidemiology of nosocomial outbreaks, of clinically significant pathogens in acute-care hospitals.

SOURCES

PubMed search with relevant keywords along with personal collection of relevant publications.

CONTENT

Representative case scenarios and critical review of the relevant scientific literature.

IMPLICATIONS

The review provides practical action plans to manage molecular epidemiologic investigations of outbreaks caused by clinically significant nosocomial pathogens, while prioritizing the use and timely integration of the various methodologies.

Acquisition and persistence of strain-specific methicillin-resistant Staphylococcus aureus and their determinants in community nursing homes

Background

Nursing home residents are frequently colonized with various strains of methicillin-resistant Staphylococcus aureus (MRSA) but the intra-facility dynamics of strain-specific MRSA remains poorly understood. We aimed at identifying and quantifying the associations between acquisition and carriage of MRSA strains and their potential risk factors in community nursing homes using mathematical modeling.

Methods

The data was collected during a longitudinal MRSA surveillance study in six nursing homes in South Central Wisconsin. MRSA cultures were obtained from subjects every 3 months for up to one year. MRSA isolates were subsequently strain-typed by pulsed-field gel electrophoresis (PFGE), and their genetic similarity was established based on the Dice coefficients. Bayesian network analysis, logistic regression and elastic net were used to quantify the associations between acquisition and carriage of MRSA strains discriminated at 80% and 95% strain similarity thresholds and potentially modifiable resident characteristics including previous antibiotic exposure, comorbidity, medical devices, chronic wounds, functional and cognitive status and recent hospitalizations.

Results

Absence of severe cognitive impairment as well as presence of a wound, device and severe comorbidity was associated with elevated probability of USA100 carriage although there was a variation based on the combination of those risk factors. Residents with severe comorbidity and cognitive status and presence of device and wound were identified as certain carriers of USA100 in our sample. Residents with a chronic wound were more likely to carry USA100 MRSA (OR = 2.77, 95% CI = 1.37–5.87). Functional status was identified as an important determinant of carriage of USA100 and USA300 strains. Comorbidity and cognitive status were the two factors associated with carriage of all clonal groups in the study (USA100, USA300 and USA1200).

Conclusions

The combination of Bayesian network analysis, logistic regression and elastic net can be used to identify associations between acquisition and carriage of MRSA strains and their potential risk factors in the face of scarce data. The revealed associations may be used to generate hypothesis for further study of determinants of acquisition and carriage of selected MRSA subtypes and to better inform infection control efforts in community nursing homes.

Electronic supplementary material

The online version of this article (10.1186/s12879-017-2837-3) contains supplementary material, which is available to authorized users.

Models to predict prevalence and transition dynamics of methicillin-resistant Staphylococcus aureus in community nursing homes

BACKGROUND

Recent spread of USA300 methicillin-resistant Staphylococcus aureus (MRSA) to nursing homes has been of particular concern. We sought to predict the ultimate prevalence of USA300 and non-USA300 MRSA and to examine the influence of potential risk factors on MRSA acquisition in community nursing homes.

METHODS

The data were collected during a longitudinal MRSA surveillance study that involved 449 residents in 6 community nursing homes in Wisconsin. The subjects were screened every 3 months for up to 1 year. Markov chain models were employed to predict strain-specific prevalence of MRSA at steady state, and to assess the influence of potential risk factors, including recent hospitalizations, invasive medical devices, and antibiotic exposure on MRSA acquisition rates and average duration of colonization.

RESULTS

At steady state, 20% (95% confidence interval [CI], 15%-25%) of residents were predicted to remain colonized with non-USA300 and 4% (95% CI, 2%-7%) with USA300 MRSA. Residents who used antibiotics during the previous 3 months were twice more likely to acquire MRSA than those who did not (acquisition rates, 0.052; 95% CI, 0.038-0.075 and 0.025; 95% CI, 0.018-0.037, respectively).

CONCLUSIONS

Non-USA300 was predicted to remain the dominant MRSA strain in community nursing homes. The higher rate of MRSA acquisition among residents with recent antibiotic exposure suggests that antibiotic stewardship may reduce MRSA colonization in this setting.

High-resolution subtyping of Staphylococcus aureus strains by means of Fourier-transform infrared spectroscopy

Staphylococcus aureus causes a variety of serious illnesses in humans and animals. Subtyping of S. aureus isolates plays a crucial role in epidemiological investigations. Metabolic fingerprinting by Fourier-transform infrared (FTIR) spectroscopy is commonly used to identify microbes at species as well as subspecies level. In this study, we aimed to assess the suitability of FTIR spectroscopy as a tool for S. aureus subtyping. To this end, we compared the subtyping performance of FTIR spectroscopy to other subtyping methods such as pulsed field gel electrophoresis (PFGE) and spa typing in a blinded experimental setup and investigated the ability of FTIR spectroscopy for identifying S. aureus clonal complexes (CC). A total of 70 S. aureus strains from human, animal, and food sources were selected, for which clonal complexes and a unique virulence and resistance gene pattern had been determined by DNA microarray analysis. FTIR spectral analysis resulted in high discriminatory power similar as obtained by spa typing and PFGE. High directional concordance was found between FTIR spectroscopy based subtypes and capsular polysaccharide expression detected by FTIR spectroscopy and the cap specific locus, reflecting strain specific expression of capsular polysaccharides and/or other surface glycopolymers, such as wall teichoic acid, peptidoglycane, and lipoteichoic acid. Supervised chemometrics showed only limited possibilities for differentiation of S. aureus CC by FTIR spectroscopy with the exception of CC45 and CC705. In conclusion, FTIR spectroscopy represents a valuable tool for S. aureus subtyping, which complements current molecular and proteomic strain typing.

Discriminatory Indices of Typing Methods for Epidemiologic Analysis of Contemporary Staphylococcus aureus Strains

Historically, a number of typing methods have been evaluated for Staphylococcus aureus strain characterization. The emergence of contemporary strains of community-associated S. aureus, and the ensuing epidemic with a predominant strain type (USA300), necessitates re-evaluation of the discriminatory power of these typing methods for discerning molecular epidemiology and transmission dynamics, essential to investigations of hospital and community outbreaks. We compared the discriminatory index of 5 typing methods for contemporary S. aureus strain characterization. Children presenting to St. Louis Children's Hospital and community pediatric practices in St. Louis, Missouri (MO), with community-associated S. aureus infections were enrolled. Repetitive sequence-based PCR (repPCR), pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), staphylococcal protein A (spa), and staphylococcal cassette chromosome (SCC) mec typing were performed on 200 S. aureus isolates. The discriminatory index of each method was calculated using the standard formula for this metric, where a value of 1 is highly discriminatory and a value of 0 is not discriminatory. Overall, we identified 26 distinct strain types by repPCR, 17 strain types by PFGE, 30 strain types by MLST, 68 strain types by spa typing, and 5 strain types by SCCmec typing. RepPCR had the highest discriminatory index (D) of all methods (D = 0.88), followed by spa typing (D = 0.87), MLST (D = 0.84), PFGE (D = 0.76), and SCCmec typing (D = 0.60). The method with the highest D among MRSA isolates was repPCR (D = 0.64) followed by spa typing (D = 0.45) and MLST (D = 0.44). The method with the highest D among MSSA isolates was spa typing (D = 0.98), followed by MLST (D = 0.93), repPCR (D = 0.92), and PFGE (D = 0.89). Among isolates designated USA300 by PFGE, repPCR was most discriminatory, with 10 distinct strain types identified (D = 0.63). We identified 45 MRSA isolates which were classified as identical by PFGE, MLST, spa typing, and SCCmec typing (USA300, ST8, t008, SCCmec IV, respectively); within this collection, there were 5 distinct strain types identified by repPCR. The typing methods yielded comparable discriminatory power for S. aureus characterization overall; when discriminating among USA300 isolates, repPCR retained the highest discriminatory power. This property is advantageous for investigations conducted in the era of contemporary S. aureus infections.

Strict infection control leads to low incidence of methicillin-resistant Staphylococcus aureus bloodstream infection over 20 years

OBJECTIVE

Methicillin-resistant Staphylococcus aureus (MRSA) is a worldwide issue associated with significant morbidity and mortality. Multiple infection control (IC) approaches have been tested to control its spread; however, the success of the majority of trials has been short-lived and many efforts have failed. We report the long-term success of MRSA control from a prospective observational study over 20 years.

SETTING

University Hospital Basel is a large tertiary care center with a median bed capacity of 855 and 5 intensive care units (ICUs); currently, the facility has >32,000 admissions per year.

METHODS

The IC program at the University Hospital Basel was created in 1993, after 2 MRSA outbreaks. The program has included strict contact precautions with single rooms for MRSA-colonized or -infected patients, targeted admission screening of high-risk patients and healthcare workers at risk for carriage, molecular typing of all MRSA strains and routine decolonization of MRSA carriers including healthcare workers. We used the incidence of MRSA bloodstream infections (BSIs) to assess the effectiveness of this program. All MRSA cases were prospectively classified using a standardized case report form in nosocomial and nonnosocomial cases, based on CDC definitions.

RESULTS

Between 1993 and 2012, 540,669 blood samples were cultured. The number of blood cultures increased from 865 per 10,000 patient days in 1993 to 1,568 per 10,000 patient days in 2012 (P<.001). We identified 1,268 episodes of S. aureus BSI from 1,204 patients. MRSA accounted for 34 episodes (2.7%) and 24 of these (1.9%) were nosocomial. MRSA BSI incidence varied between 0 and 0.27 per 10,000 patient days and remained stable with no significant variation throughout the study period (P=.882).

CONCLUSIONS

Long-term control of MRSA is feasible when a bundle of IC precautions is strictly enforced over time.