Utility of spa typing for investigating the local epidemiology of MRSA on a UK intensive care ward

Methicillin-Resistant Staphylococcus aureus in Seafood: Prevalence, Laboratory Detection, Clonal Nature, and Control in Seafood Chain

Methicillin-resistant Staphylococcus aureus (MRSA), a versatile pathogen bearing multiple virulence determinants, is increasingly being detected in various food-producing animals, including fish. In addition, it is a potential food poisoning agent. MRSA is not an inherent microbiota of fish; its presence is attributed to pre- or postharvest contamination through fish handlers, water, ice, and processing equipment. Several reviews have been written on MRSA in clinical as well as the food animal-producing sector, but information specific to MRSA in seafood is scant. This review puts forth insights on MRSA detection in seafood, antibiotic resistance, diversity of clones in seafood, and possible control measures in seafood production chain. Emphasis has been given on assessing the variations in the protocols employed for isolation and identification in different food matrices and lay the foundation for researchers to develop optimized procedure.

Transmission pathways of multidrug-resistant organisms in the hospital setting: a scoping review

BACKGROUND

Prevalence of multidrug-resistant microorganisms (MDROs) continues to increase, while infection control gaps in healthcare settings facilitate their transmission between patients. In this setting, 5 distinct yet interlinked pathways are responsible for transmission. The complete transmission process is still not well understood. Designing and conducting a single research study capable of investigating all 5 complex and multifaceted pathways of hospital transmission would be costly and logistically burdensome. Therefore, this scoping review aims to synthesize the highest-quality published literature describing each of the 5 individual potential transmission pathways of MDROs in the healthcare setting and their overall contribution to patient-to-patient transmission.

METHODS

In 3 databases, we performed 2 separate systematic searches for original research published during the last decade. The first search focused on MDRO transmission via the HCW or the environment to identify publications studying 5 specific transmission pathways: (1) patient to HCW, (2) patient to environment, (3) HCW to patient, (4) environment to patient, and (5) environment to HCW. The second search focused on overall patient-to-patient transmission regardless of the transmission pathway. Both searches were limited to transmission of methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus, multidrug-resistant A. baumannii, and carbapenem-resistant Enterobacteriaceae. After abstract screening of 5,026 manuscripts, researchers independently reviewed and rated the remaining papers using objective predefined criteria to identify the highest quality and most influential manuscripts.

RESULTS

High-quality manuscripts were identified for all 5 routes of transmission. Findings from these studies were consistent for all pathways; however, results describing the routes from the environment/HCW to a noncolonized patient were more limited and variable. Additionally, most research focused on MRSA, instead of other MDROs. The second search yielded 10 manuscripts (8 cohort studies) that demonstrated the overall contribution of patient-to-patient transmission in hospitals regardless of the transmission route. For MRSA, the reported cross-transmission was as high as 40%.

CONCLUSIONS

This scoping review brings together evidence supporting all 5 possible transmission pathways and illustrates the complex nature of patient-to-patient transmission of MDROs in hospitals. Our findings also confirm that transmission of MDROs in hospitals occurs frequently, suggesting that ongoing efforts are necessary to strengthen infection prevention and control to prevent the spread of MDROs.

Nasal colonisation, antimicrobial susceptibility and genotypic pattern of Staphylococcus aureus among agricultural biotechnology students in Besut, Terengganu, east coast of Malaysia

BACKGROUND

This study aimed to profile the antimicrobial susceptibility and presence of resistance and virulence genes of methicillin-susceptible Staphylococcus aureus (MSSA) and MRSA nasal carriage, by means of genotypic analyses, in students of a tertiary institution in the state of Terengganu, east coast of Malaysia.

METHODS

A total of 370 agricultural biotechnology students from Universiti Sultan Zainal Abidin in Besut, Terengganu, were enrolled in this study. Antimicrobial susceptibility profiles were evaluated by standard methods. PCR detection of resistance and virulence genes was performed on S. aureus that were methicillin-resistant, macrolide-lincosamide-streptogramin B (MLS_B )-positive phenotype and/or positive for the leukocidin (pvl) gene followed by staphylococcal cassette chromosome mec (SCCmec), staphylococcal protein A (spa) and accessory gene regulator (agr) typing.

RESULTS

One hundred and nineteen of 370 students carried S. aureus (32%); 18 of the isolates were MRSA (15%). Erythromycin resistance was detected in 20% (24/119) of which 15% (18/119) were MRSA and 5% (6/119) MSSA. Among the 24 erythromycin-resistant isolates, D-test was positive in 29% (7/24) displaying inducible MLS_B , whereas the remaining 71% (17/24) showed constitutive MLS_B phenotypes. Nine (7.6%) of 119 isolates were pvl positive: 44% MRSA (4/9) and 56% MSSA (5/9). Staphylococcal surface protein sasX gene was present in 92% of MRSA and 8% of MSSA isolates. The majority of MRSA isolates were agr type I (15/18; 83%). Five spa types identified with spa t037 were predominant, followed by spa types (t304 and t8696) as newly reported Malaysian MRSA in a community setting.

CONCLUSION

The presence of MRSA with SCCmec of hospital-associated features and globally recognised spa types in community setting is worrisome. Furthermore, the presence of MLS_B strains among multidrug-resistant (MDR) S. aureus with sasX as well as pvl-positive isolates highlights the potential risk of a community setting in facilitating the dissemination of both virulence and resistance determinants.

Distribution of the Most Prevalent Spa Types among Clinical Isolates of Methicillin-Resistant and -Susceptible Staphylococcus aureus around the World: A Review

Background:Staphylococcus aureus, a leading cause of community-acquired and nosocomial infections, remains a major health problem worldwide. Molecular typing methods, such as spa typing, are vital for the control and, when typing can be made more timely, prevention of S. aureus spread around healthcare settings. The current study aims to review the literature to report the most common clinical spa types around the world, which is important for epidemiological surveys and nosocomial infection control policies.

Methods: A search via PubMed, Google Scholar, Web of Science, Embase, the Cochrane library, and Scopus was conducted for original articles reporting the most prevalent spa types among S. aureus isolates. The search terms were “Staphylococcus aureus, spa typing.”

Results: The most prevalent spa types were t032, t008 and t002 in Europe; t037 and t002 in Asia; t008, t002, and t242 in America; t037, t084, and t064 in Africa; and t020 in Australia. In Europe, all the isolates related to spa type t032 were MRSA. In addition, spa type t037 in Africa and t037and t437 in Australia also consisted exclusively of MRSA isolates. Given the fact that more than 95% of the papers we studied originated in the past decade there was no option to study the dynamics of regional clone emergence.

Conclusion: This review documents the presence of the most prevalent spa types in countries, continents and worldwide and shows big local differences in clonal distribution.

Epidemiology and spa-type diversity of meticillin-resistant Staphylococcus aureus in community and healthcare settings in Norway

BACKGROUND

There has been a marked increase in the incidence of meticillin-resistant Staphylococcus aureus (MRSA) during the past decade in Norway; a country with one of the lowest prevalence rates and an active 'search-and-destroy' policy applied to hospital settings.

AIM

To characterize the trends of notification rates of community-associated (CA) and healthcare-associated (HA) MRSA in Norway, and explore the diversity and circulation of MRSA spa types within and outside healthcare settings.

METHODS

A registry-based study on notified MRSA infections and colonizations was conducted in Norway between 2006 and 2015. The diversity and abundance of CA- and HA-MRSA spa types were compared using novel ecological diversity measures (Hill numbers).

FINDINGS

During the study period, the monthly notification rate increased 6.9-fold and 1.8-fold among CA- and HA-MRSA, respectively; the increase was steeper among colonizations than infections. In both settings, the distribution of spa types was uneven, with a few dominant spa types and many singletons. The spa-type diversity of CA-MRSA was higher than HA-MRSA in terms of different types (685 vs 481), and increased during the study period. However, the diversity associated with the dominant spa types was similar and remained stable. A high overlap of spa types was estimated between the settings; spa-t002, t019 and t008 were the most common.

CONCLUSION

The present findings suggest a strong connection between CA- and HA-MRSA epidemiology in Norway. If the fast-growing trend of CA-MRSA continues in the years to come, it may challenge current guidelines and infection control of MRSA in healthcare environments.

Multiple-locus variable number tandem repeat analysis is superior to spa typing and sufficient to characterize MRSA for surveillance purposes

AIM

Assess the best approach to type methicillin-resistant Staphylococcus aureus (MRSA), Staphylococcal protein A (spa) typing, multiple-locus variable number tandem repeat analysis (MLVA) or both.

MATERIALS & METHODS

Discriminatory power of spa typing and MLVA was determined using 20,771 MRSA isolates.

RESULTS

There were twice as many MLVA types (MTs) as spa types present in the collection. Among the top 70% of the isolates, 37 spa types and 139 MTs were found. MLVA diversity among the top-10 spa types was high (diversity index 0.96), while spa diversity among the top-10 MTs was much lower (diversity index 0.83). The probability that two MRSA isolates with the same spa type also had the same MT was low (Wallace's coefficient 0.27). By contrast, most MRSA isolates yielding the same MT also had the same spa type (Wallace's coefficient 0.90).

CONCLUSION

MLVA is superior to spa typing and will suffice to characterize MRSA isolates for surveillance.

Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common healthcare-associated pathogens. To examine the role of inter-hospital patient sharing on MRSA transmission, a previous study collected 2,214 samples from 30 hospitals in Orange County, California and showed by spa typing that genetic differentiation decreased significantly with increased patient sharing. In the current study, we focused on the 986 samples with spa type t008 from the same population.

Methods

We used genome sequencing to determine the effect of patient sharing on genetic differentiation between hospitals. Genetic differentiation was measured by between-hospital genetic diversity, F_ST, and the proportion of nearly identical isolates between hospitals.

Results

Surprisingly, we found very similar genetic diversity within and between hospitals, and no significant association between patient sharing and genetic differentiation measured by F_ST. However, in contrast to F_ST, there was a significant association between patient sharing and the proportion of nearly identical isolates between hospitals. We propose that the proportion of nearly identical isolates is more powerful at determining transmission dynamics than traditional estimators of genetic differentiation (F_ST) when gene flow between populations is high, since it is more responsive to recent transmission events. Our hypothesis was supported by the results from coalescent simulations.

Conclusions

Our results suggested that there was a high level of gene flow between hospitals facilitated by patient sharing, and that the proportion of nearly identical isolates is more sensitive to population structure than F_ST when gene flow is high.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-016-0274-3) contains supplementary material, which is available to authorized users.

Rapid, highly discriminatory binary genotyping to demonstrate methicillin-resistant Staphylococcus aureus transmission in a tertiary care intensive care unit

OBJECTIVES

No previous studies of methicillin-resistant Staphylococcus aureus (MRSA) epidemiology in adult intensive care units (ICUs) have assessed the utility of rapid, highly discriminatory strain typing in the investigation of transmission events.

DESIGN

Observational.

SETTING

A 22-bed medical-surgical adult ICU. Patients Those admissions MRSA-positive on initial screening and all admissions <48 hours in duration were excluded, leaving a cohort of 653 patients (median age, 61 years; APACHE-II, 19).

METHODS

We conducted this study of MRSA transmission over 1 year (August 1, 2011 to July 31, 2012) using a multiplex PCR-based reverse line blot (mPCR/RLB) assay to genotype isolates from surveillance swabs obtained at admission and twice weekly during ICU stays. MRSA prevalence and incidence rates were calculated and transmission events were identified using strain matching. Colonization pressure was calculated daily by summation of all MRSA cases.

RESULTS

Of 1,030 admissions to ICU during the study period, 349 patients were excluded. MRSA acquisition occurred during 31 of 681 (4.6%) remaining admissions; 19 of 31(61%) acquisitions were genotype-confirmed, including 7 (37%) due to the most commonly transmitted strain. Moving averages of MRSA patient numbers on the days prior to a documented event were used in a Poisson regression model. A significant association was found between transmission and colonization pressure when the average absolute colonization pressure on the previous day was ≥3 (χ2=7.41, P=0.01).

CONCLUSIONS

mPCR/RLB characterizes MRSA isolates within a clinically useful time frame for identification of single-source clusters within the ICU. High MRSA colonization pressure (≥3 MRSA-positive patients) on a given day is associated with an increased likelihood of a transmission event.

spa typing alone is not sufficient to demonstrate endemic establishment of meticillin-resistant Staphylococcus aureus in a low-prevalence country

BACKGROUND

The prevalence of meticillin-resistant Staphylococcus aureus (MRSA) in Norway is low but increasing. Over the last decade, numerous nursing homes have experienced MRSA outbreaks. One genetic lineage, spa type t304, has been identified at multiple nursing homes and has caused large outbreaks lasting for several years.

AIM

To evaluate whether spa typing is sufficient for the detection of MRSA spread and endemic establishment in a low-prevalence area, using spa type t304 as the test organism.

METHODS

All spa type t304 isolates detected in 1991-2010 in the most densely populated area of Norway were included. Time and place of bacterial sampling were recorded. The isolates were analysed using multi-locus sequence typing, staphylococcal cassette chromosome mec typing, detection of lukS/F-PV and pulsed-field gel electrophoresis (PFGE).

FINDINGS

In total, 181 spa type t304 isolates were identified in three of 23 municipalities. Most (91%) of the isolates could be linked to 13 nursing homes, eight of which experienced outbreaks. PFGE analysis revealed three PFGE types, consisting of 19 PFGE patterns; 95% of the isolates were PFGE type 2. In total, PFGE types 2 and 3 accounted for 99% of all nursing home isolates, and included isolates from different nursing homes, different outbreaks and different time periods. Additional genetic analyses did not further differentiate between the spa type t304 isolates.

CONCLUSION

MRSA spa type t304 appears to have established itself as an endemic genetic lineage in the study area. spa typing does not provide sufficient resolution when investigating the spread of an endemic-like genetic lineage in a low-prevalence area, and should be supplemented by additional typing techniques.

Genome-wide single nucleotide polymorphism-based assay for high-resolution epidemiological analysis of the methicillin-resistant Staphylococcus aureus hospital clone EMRSA-15

The EMRSA-15 clone is a major cause of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) infections in the UK and elsewhere but existing typing methodologies have limited capacity to discriminate closely related strains, and are often poorly reproducible between laboratories. Here, we report the design, development and validation of a genome-wide single nucleotide polymorphism (SNP) typing method and compare it to established methods for typing of EMRSA-15. In order to identify discriminatory SNPs, the genomes of 17 EMRSA-15 strains, selected to represent the breadth of genotypic and phenotypic diversity of EMRSA-15 isolates in Scotland, were determined and phylogenetic reconstruction was carried out. In addition to 17 phylogenetically informative SNPs, five binary markers were included to form the basis of an EMRSA-15 genotyping assay. The SNP-based typing assay was as discriminatory as pulsed-field gel electrophoresis, and significantly more discriminatory than staphylococcal protein A (spa) typing for typing of a representative panel of diverse EMRSA-15 strains, isolates from two EMRSA-15 hospital outbreak investigations, and a panel of bacteraemia isolates obtained in healthcare facilities in the east of Scotland during a 12-month period. The assay is a rapid, and reproducible approach for epidemiological analysis of EMRSA-15 clinical isolates in Scotland. Unlike established methods the DNA sequence-based method is ideally suited for inter-laboratory comparison of identified genotypes, and its flexibility lends itself to supplementation with additional SNPs or markers for the identification of novel S. aureus strains in other regions of the world.

Epidemiology of MRSA in southern Sweden: strong relation to foreign country of origin, health care abroad and foreign travel

All notified MRSA cases in Skåne County have been followed since 2000. We have investigated the MRSA epidemiology over time, method of acquisition, whether some spa types are more prone to spread, and/or cause more infections, and the connection between spa type and country of acquisition/origin. All cases between 2000 and 2010 were included. Infection or colonization and the presence of PVL genes were noted. The spa types of the index cases were correlated with community or healthcare acquisition, proportion of MRSA-positive household contacts, country of origin of families and country of acquisition of MRSA. The number of cases increased from 31 in 2000 to 315 in 2010. Most cases were community-acquired and the median age was 30 years. Thirty-two per cent of the MRSA cases were found because of a clinical infection. Of the household contacts 35 % were MRSA-positive. Only 24 % of the MRSA cases were both of Swedish origin and had contracted MRSA in Sweden. An association between spa type and certain regions of acquisition/origin was noted. Spa types t044, t002 and t008 were the most predominant strains. PVL-positive spa types t008, t019 and t044 caused more skin infections than the other spa types. Our results support screening for MRSA in patients with health care contacts abroad, culturing of patients with skin infections contracted outside Sweden and performing contact tracing among household members. Knowledge of spa type might give guidance in the process of contact tracing. Eradication treatment of MRSA spa types causing more skin infections may be warranted.

Molecular characterization of Staphylococcus aureus from patients with surgical site infections at Mulago Hospital in Kampala, Uganda

BACKGROUND

The prevalence of Methicillin resistant Staphylococcus aureus (MRSA) is progressively increasing globally with significant regional variation. Understanding the Staphylococcus aureus lineages is crucial in controlling nosocomial infections. Recent studies on S. aureus in Uganda have revealed an escalating burden of MRSA. However, the S. aureus genotypes circulating among patients are not known. Here, we report S. aureus lineages circulating in patients with surgical site infections (SSI) at Mulago National hospital, Kampala, Uganda.

METHODS

A cross-sectional study involving 314 patients with SSI at Mulago National Hospital was conducted from September 2011 to April 2012. Pus swabs from the patients' SSI were processed using standard microbiological procedures. Methicillin sensitive Staphylococcus aureus (MSSA) and MRSA were identified using phenotypic tests and confirmed by PCR-detection of the nuc and mecA genes, respectively. SCCmec genotypes were determined among MRSA isolates using multiplex PCR. Furthermore, to determine lineages, spa sequence based-genotyping was performed on all S. aureus isolates.

RESULTS

Of the 314 patients with SSI, S. aureus accounted for 20.4% (64/314), of which 37.5% (24/64) were MRSA. The predominant SCCmec types were type V (33.3%, 8/24) and type I (16.7%, 4/24). The predominant spa lineages were t645 (17.2%, 11/64) and t4353 (15.6%, 10/64), and these were found to be clonally circulating in all the surgical wards. On the other hand, lineages t064, t355, and t4609 were confined to the obstetrics and gynecology wards. A new spa type (t10277) was identified from MSSA isolate. On multivariate logistic regression analysis, cancer and inducible clindamycin resistance remained as independent predictors of MRSA-SSI.

CONCLUSION

SCCmec types I and V are the most prevalent MRSA mecA types from the patients' SSI. The predominant spa lineages (t645 and t4353) are clonally circulating in all the surgical wards, calling for strengthening of infection control practices at Mulago National Hospital.

Outbreak of Staphylococcal food poisoning due to SEA-producing Staphylococcus aureus

In 2008, 150 people gathered for a wedding celebration in Baden-Württemberg, Germany. Three hours after ingestion of a variety of foods including pancakes filled with minced chicken, several guests exhibited symptoms of acute gastroenteritis such as vomiting, diarrhea, fever, and ague. Twelve guests were reported to have fallen ill, with nine of these seeking medical care in hospitals. At least four patients were admitted to the hospital and received inpatient treatment, among them a 2-year-old child and a woman in the 4th month of pregnancy. Within 24 h of the event, an investigative team collected a variety of samples including refrigerated leftovers, food in the storage unit of the caterer, nasal swabs of the caterer, as well as 21 environmental swabs. Five stool samples from patients were provided by the hospitals. Staphylococcus aureus isolates were gathered from eight samples, among them nasal swabs of the caterer, food samples, and one stool sample. Fourier transform-infrared spectroscopy was used for species identification and for primary clustering of the isolates in a similarity tree. The isolates were further characterized by spa typing and pulsed-field gel electrophoresis, and a DNA microarray was used to determine the presence/absence of genes involved in virulence and antimicrobial resistance. We were able to match an enterotoxigenic strain from the stool sample of a patient to isolates of the same strain obtained from food and the nasal cavity of a food handler. The strain produced the enterotoxin SEA and the toxic shock syndrome toxin-1, and was also found to exhibit the genes encoding enterotoxins SEG and SEI, as well as the enterotoxin gene cluster egc. This is one of only a few studies that were able to link a staphylococcal food poisoning outbreak to its source.

MRSA transmission on a neonatal intensive care unit: epidemiological and genome-based phylogenetic analyses

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) may cause prolonged outbreaks of infections in neonatal intensive care units (NICUs). While the specific factors favouring MRSA spread on neonatal wards are not well understood, colonized infants, their relatives, or health-care workers may all be sources for MRSA transmission. Whole-genome sequencing may provide a new tool for elucidating transmission pathways of MRSA at a local scale.

METHODS AND FINDINGS

We applied whole-genome sequencing to trace MRSA spread in a NICU and performed a case-control study to identify risk factors for MRSA transmission. MRSA genomes had accumulated sequence variation sufficiently fast to reflect epidemiological linkage among individual patients, between infants and their mothers, and between infants and staff members, such that the relevance of individual nurses' nasal MRSA colonization for prolonged transmission could be evaluated. In addition to confirming previously reported risk factors, we identified an increased risk of transmission from infants with as yet unknown MRSA colonisation, in contrast to known MRSA-positive infants.

CONCLUSIONS

The integration of epidemiological (temporal, spatial) and genomic data enabled the phylogenetic testing of several hypotheses on specific MRSA transmission routes within a neonatal intensive-care unit. The pronounced risk of transmission emanating from undetected MRSA carriers suggested that increasing the frequency or speed of microbiological diagnostics could help to reduce transmission of MRSA.

Harnessing the genome: development of a hierarchical typing scheme for meticillin-resistant Staphylococcus aureus

A major barrier to using genome sequencing in medical microbiology is the ability to interpret the data. New schemes that provide information about the importance of sequence variation in both clinical and public health settings are required. Meticillin-resistant Staphylococcus aureus (MRSA) is an important nosocomial pathogen that is being observed with increasing frequency in community settings. Better tools are needed to improve our understanding of its transmissibility and micro-epidemiology in order to develop effective interventions. Using DNA microarray technology we identified a set of 20 binary targets whose presence or absence could be determined by PCR, producing a PCR binary typing scheme (PCR-BT). This was combined with multi-locus sequence type-based, sequence nucleotide polymorphism typing to form a hierarchical typing scheme. When applied to a set of epidemiologically unrelated isolates, a high degree of concordance was observed with PFGE (98.8 %). The scheme was able to detect the presence or absence of an outbreak strain in eight out of nine outbreak investigations, demonstrating epidemiological concordance. PCR-BT was better than PFGE at distinguishing between outbreak strains, particularly where epidemic MRSA-15 was involved. The method developed here is a rapid, digital typing scheme for S. aureus for use in both micro- and macro-epidemiological investigations that has the advantage of being suitable for use in routine diagnostic laboratories. The targets are defined and therefore the types can be defined by any platform capable of detecting the sequences used, including whole genome sequencing.

Molecular characterization of Staphylococcus aureus isolated from children with adenoid hypertrophy: emergence of new spa types t7685 and t7692

OBJECTIVE

Adenoids have been associated with the pathogenesis of acute, recurrent and chronic infectious diseases of the upper respiratory system and their hypertrophy is one of the most common causes of upper airway obstruction affecting children. In this study, the characteristics of Staphylococcus aureus isolates from patients who had undergone adenoidectomy were investigated via spa typing method.

METHODS

A total of 113 children with adenoid hypertrophy who underwent adenoidectomy during September 2009 to November 2010, were included in the study. The isolates were identified to the species level as S. aureus using standard biochemical methods, following which the amplification and sequencing of the spa gene X region were carried out.

RESULTS

S. aureus was found in the adenoid tissue of 26 (23%) patients. Out of the 26 S. aureus isolates, 5 (19%), 3 (11.5%) and 3 (11.5%) were resistant to tetracycline, erythromycin and oxacillin respectively. All the isolates were susceptible to vancomycin, rifampin, ciprofloxacin, gentamicin, mupirocin and quinupristin-dalfopristin and were typed using spa typing method. All the isolates were found to include 21 spa types, including two previously unreported types (t7685 and t7692). The most prevalent spa types were t7685 (11.5%), t230 (8%), t325 (8%) and t1149 (8%).

CONCLUSION

This study demonstrates that the prevalence rate of S. aureus in the adenoid tissue of the children assessed was 23%. An interesting point to note was the dominance of the spa type t7685 that has not been previously reported by other studies.

From types to trees: reconstructing the spatial spread of Staphylococcus aureus based on DNA variation

Tracing the spatial spread of pathogens is a key objective of molecular infectious disease epidemiology. Accordingly, a wide range of genotyping approaches have been used to monitor the dissemination of Staphylococcus aureus strains, from localized outbreaks to global spread. We provide a critical review of available methods, revealing that molecular markers currently in use for typing S. aureus acquire changes so slowly that they monitor evolutionary change over timescales that are largely irrelevant to epidemiology. Moreover, the more variable markers frequently do not reflect the pathogen's evolutionary history and, hence, provide potentially misleading information about spread. More recent work has demonstrated that staphylococcal evolution proceeds sufficiently fast that the dynamics of S. aureus spatial spread can be elucidated at great detail on the basis of genome-wide single-nucleotide polymorphisms.

Cross-sectional study of antimicrobial-resistant bacteria in horses. Part 1: Prevalence of antimicrobial-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus

REASONS FOR PERFORMING STUDY

The increasing prevalence of antimicrobial-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) and antimicrobial-resistant Escherichia coli represents a significant problem. However, the carriage of such bacteria by horses in the UK has not been well characterised.

OBJECTIVES

To estimate the prevalence of nasal carriage of MRSA and faecal carriage of antimicrobial-resistant E. coli amongst horses in the general equine community of the mainland UK.

METHODS

A cross-sectional study of horses recruited by 65 randomly selected equine veterinary practices was conducted, with nasal swabs and faecal samples collected. Faecal samples were cultured for antimicrobial-resistant E. coli. Nasal swabs were cultured for staphylococcal species; methicillin-resistant isolates identified as S. aureus were characterised by SCCmec and spa gene typing. Multilevel logistic regression models were used to calculate prevalence estimates with adjustment for clustering at practice and premises levels. Spatial variation in risk of antimicrobial resistance was also examined.

RESULTS

In total, 650 faecal samples and 678 nasal swabs were collected from 692 horses located on 525 premises. The prevalence of faecal carriage of E. coli with resistance to any antimicrobial was 69.5% (95% CI 65.9-73.1%) and the prevalence of extended-spectrum β-lactamase (ESBL)-producing E. coli was 6.3% (95% CI 4.1-9.6%). The prevalence of nasal carriage of MRSA was 0.6% (95% CI 0.2-1.5%). Spatial analysis indicated variation across the UK for risk of carriage of resistant and multidrug-resistant (resistant to more than 3 antimicrobial classes) E. coli.

CONCLUSIONS AND POTENTIAL RELEVANCE

Carriage of MRSA by horses in the community appears rare, but the prevalence of antimicrobial-resistant E. coli (including ESBL-producing E. coli) is higher. A high prevalence of antimicrobial-resistant bacteria could have significant health implications for the horse population of the UK.

Comparison of Staphylococcus aureus isolates associated with food intoxication with isolates from human nasal carriers and human infections

Staphylococcus aureus represents an organism of striking versatility. While asymptomatic nasal colonization is widespread, it can also cause serious infections, toxinoses and life-threatening illnesses in humans and animals. Staphylococcal food poisoning (SFP), one of the most prevalent causes of foodborne intoxication worldwide, results from oral intake of staphylococcal enterotoxins leading to violent vomiting, diarrhea and cramps shortly upon ingestion. The aim of the present study was to compare isolates associated with SFP to isolates collected from cases of human nasal colonization and clinical infections in order to investigate the role of S. aureus colonizing and infecting humans as a possible source of SFP. Spa typing and DNA microarray profiling were used to characterize a total of 120 isolates, comprising 50 isolates collected from the anterior nares of healthy donors, 50 isolates obtained from cases of clinical infections in humans and 20 isolates related to outbreaks of staphylococcal food poisoning. Several common spa types were found among isolates of all three sources (t015, t018, t056, t084). DNA microarray results showed highly similar virulence gene profiles for isolates from all tested sources. These results suggest contamination of foodstuff with S. aureus colonizing and infecting food handlers to represent a source of SFP.

Studying the transmission dynamics of meticillin-resistant Staphylococcus aureus in Hong Kong using spa typing

This study investigated the transmission dynamics of meticillin-resistant Staphylococcus aureus (MRSA) in a tertiary referral surgical unit with 300 beds. All adult patients were actively screened for MRSA by culture at hospital admission and twice weekly thereafter during hospitalisation from 1 October to 31 December 2008. The colonisation pressure per 1000 patient-days and the incidence density of nosocomial MRSA transmission per 1000 colonisation-days were calculated for the different spa types of MRSA. In total, 6619 nasal swabs were obtained from 2289 patients. One-hundred and forty-eight (7%) patients had MRSA in nasal swabs at admission screening, of which 68/148 (46%) were residents of elderly care homes. Fifty-two of 2141 (2%) patients had conversion of nasal MRSA carriage status from negative to positive during hospitalisation. Among the 200 patients with MRSA, spa types t1081 and t037 were found in 99 (50%) and 30 (15%) patients, respectively. The colonisation pressure per 1000 patient-days was 40.9 for t0181, 22.2 for t037 and 26.3 for the less common spa types. The incidence densities of nosocomial MRSA transmission per 1000 colonisation-days were significantly higher for t1081 (28.5 vs 4.0, P<0.01) and t037 (21.5 vs 4.0, P=0.03) compared with the less common spa types. Proactive screening of MRSA in patients from elderly care homes and targeted isolation of these patients, especially those carrying spa types with high transmissibility, are important for the control of MRSA in hospitals.

Comparison of two multilocus variable-number tandem-repeat methods and pulsed-field gel electrophoresis for differentiating highly clonal methicillin-resistant Staphylococcus aureus isolates

In the United Kingdom, EMRSA-15 and EMRSA-16 account for the majority (∼90%) of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) infections. Currently, the standard typing technique, pulsed-field gel electrophoresis (PFGE), is laborious and insufficient for discriminating between closely related subtypes of EMRSA-15 and -16. The objective of the present study was to compare the usefulness of multilocus variable-number tandem-repeat fingerprinting (MLVF) and multilocus variable-number tandem-repeat analysis (MLVA) with PFGE for subtyping these highly clonal MRSA lineages. A panel of 85 MRSA isolates (41 EMRSA-15, 20 EMRSA-16, and 24 MRSA isolates with diverse PFGE patterns) was investigated. In addition, a further 29 EMRSA-15s with identical PFGE patterns from two geographically linked but epidemiologically distinct outbreaks and several sporadic cases were analyzed. PFGE, MLVF, and MLVA resolved 66 (Simpson's index of diversity [SID] = 0.984), 51 (SID = 0.95), and 42 (SID = 0.881) types, respectively, among the 85 MRSA isolates. MLVF was more discriminatory than MLVA for EMRSA-15 and -16 strains, but both methods had comparable discriminatory powers for distinguishing isolates in the group containing diverse PFGE types. MLVF was comparable to PFGE for resolving the EMRSA-15s but had a lower discriminatory power for the EMRSA-16s. MLVF and MLVA resolved the 29 isolates with identical PFGE patterns into seven and six subtypes, respectively. Importantly, both assays indicated that the two geographically related outbreaks were caused by distinct subtypes of EMRSA-15. Taken together, the data suggest that both methods are suitable for identifying and tracking specific subtypes of otherwise-indistinguishable MRSA. However, due to its greater discriminatory power, MLVF would be the most suitable alternative to PFGE for hospital outbreak investigations.

Enhanced discrimination of highly clonal ST22-methicillin-resistant Staphylococcus aureus IV isolates achieved by combining spa, dru, and pulsed-field gel electrophoresis typing data

ST22-methicillin-resistant Staphylococcus aureus type IV (ST22-MRSA-IV) is endemic in Irish hospitals and is designated antibiogram-resistogram type-pulsed-field group (AR-PFG) 06-01. Isolates of this highly clonal strain exhibit limited numbers of pulsed-field gel electrophoresis (PFGE) patterns and spa types. This study investigated whether combining PFGE and spa typing with DNA sequencing of the staphylococcal cassette chromosome mec element (SCCmec)-associated direct repeat unit (dru typing) would improve isolate discrimination. A total of 173 MRSA isolates recovered in one Irish hospital during periods in 2007 and 2008 were investigated using antibiogram-resistogram (AR), PFGE, spa, dru, and SCCmec typing. Isolates representative of each of the 17 pulsed-field group 01 (PFG-01) spa types identified underwent multilocus sequence typing, and all isolates were ST22. Ninety-seven percent of isolates (168 of 173) exhibited AR-PFG 06-01 or closely related AR patterns, and 163 of these isolates harbored SCCmec type IVh. The combination of PFGE, spa, and dru typing methods significantly improved discrimination of the 168 PFG-01 isolates, yielding 65 type combinations with a Simpson's index of diversity (SID) of 96.53, compared to (i) pairwise combinations of spa and dru typing, spa and PFGE typing, and dru and PFGE typing, which yielded 37, 44, and 43 type combinations with SIDs of 90.84, 91.00, and 93.57, respectively, or (ii) individual spa, dru, and PFGE typing methods, which yielded 17, 17, and 21 types with SIDs of 66.9, 77.83, and 81.34, respectively. Analysis of epidemiological information for a subset of PFG-01 isolates validated the relationships inferred using combined PFGE, spa, and dru typing data. This approach significantly enhances discrimination of ST22-MRSA-IV isolates and could be applied to epidemiological investigations of other highly clonal MRSA strains.