Dataset Information

Inference and control of the nosocomial transmission of methicillin-resistant Staphylococcus aureus.

ABSTRACT: Methicillin-resistant Staphylococcus aureus (MRSA) is a continued threat to human health in both community and healthcare settings. In hospitals, control efforts would benefit from accurate estimation of asymptomatic colonization and infection importation rates from the community. However, developing such estimates remains challenging due to limited observation of colonization and complicated transmission dynamics within hospitals and the community. Here, we develop an inference framework that can estimate these key quantities by combining statistical filtering techniques, an agent-based model, and real-world patient-to-patient contact networks, and use this framework to infer nosocomial transmission and infection importation over an outbreak spanning 6 years in 66 Swedish hospitals. In particular, we identify a small number of patients with disproportionately high risk of colonization. In retrospective control experiments, interventions targeted to these individuals yield a substantial improvement over heuristic strategies informed by number of contacts, length of stay and contact tracing.

SUBMITTER: Pei S

PROVIDER: S-EPMC6298769 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Inference and control of the nosocomial transmission of methicillin-resistant <i>Staphylococcus aureus</i>.

Pei Sen S Morone Flaviano F Liljeros Fredrik F Makse Hernán H Shaman Jeffrey L JL

eLife 20181218

Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) is a continued threat to human health in both community and healthcare settings. In hospitals, control efforts would benefit from accurate estimation of asymptomatic colonization and infection importation rates from the community. However, developing such estimates remains challenging due to limited observation of colonization and complicated transmission dynamics within hospitals and the community. Here, we develop an inference framework ...[more]

PMID: 30560786

Similar Datasets

Project description:UnlabelledLivestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) was detected in 2003 and rapidly became the predominant MRSA clade in the Netherlands. Studies have shown that transmissions are difficult to identify, since this MRSA variant represents a genetically homogenous clade when current typing techniques are used. Here, next-generation sequencing was performed on 206 LA-MRSA isolates to assess the capability of LA-MRSA to be transmitted between humans. The usefulness of single nucleotide variants (SNVs), the composition of the SCCmec region, and the presence of plasmids to identify transmission of LA-MRSA were assessed. In total, 30 presumed putative nosocomial transmission events and 2 LA-MRSA outbreaks were studied; in most cases, SNV analysis revealed that the isolates of the index patient and the contact(s) clustered closely together. In three presumed events, the isolates did not cluster together, indicating that transmission was unlikely. The composition of the SCCmec region corroborated these findings. However, plasmid identification did not support our SNV analysis, since different plasmids were present in several cases where SNV and SCCmec analysis suggested that transmission was likely. Next-generation sequencing shows that transmission of LA-MRSA does occur in Dutch health care settings. Transmission was identified based on SNV analysis combined with epidemiological data and in the context of epidemiologically related and unrelated isolates. Analysis of the SCCmec region provided limited, albeit useful, information to corroborate conclusions on transmissions, but plasmid identification did not.ImportanceIn 2003, a variant of methicillin-resistant Staphylococcus aureus (MRSA) isolated from pigs was also found in pig farmers in France and the Netherlands. Soon thereafter, this livestock-associated MRSA (LA-MRSA) was identified in many other countries. Transmission of LA-MRSA between humans, particularly in the health care setting, is regarded to occur sporadically. Moreover, studies that describe LA-MRSA transmission used molecular characterization of isolates with limited discriminatory power, making the validity of the conclusion that transmission occurred questionable. In our study, we sequenced the complete genomes of 206 LA-MRSA isolates, obtained from more than 30 presumed LA-MRSA transmission events. Analysis of the data showed that transmission of LA-MRSA between humans had indeed occurred in more than 90% of these events. We conclude that transmission of LA-MRSA between humans does occur in Dutch health care settings; therefore, a decision to discontinue the search and destroy policy for LA-MRSA should be taken with caution.

Project description:Rapid detection and differentiation of methicillin-resistant Staphylococcus aureus (MRSA) are critical for the early diagnosis of difficult-to-treat nosocomial and community acquired clinical infections and improved epidemiological surveillance. We developed a microfluidics chip coupled with surface enhanced Raman scattering (SERS) spectroscopy (532 nm) "lab-on-a-chip" system to rapidly detect and differentiate methicillin-sensitive S. aureus (MSSA) and MRSA using clinical isolates from China and the United States. A total of 21 MSSA isolates and 37 MRSA isolates recovered from infected humans were first analyzed by using polymerase chain reaction (PCR) and multilocus sequence typing (MLST). The mecA gene, which refers resistant to methicillin, was detected in all the MRSA isolates, and different allelic profiles were identified assigning isolates as either previously identified or novel clones. A total of 17 400 SERS spectra of the 58 S. aureus isolates were collected within 3.5 h using this optofluidic platform. Intra- and interlaboratory spectral reproducibility yielded a differentiation index value of 3.43-4.06 and demonstrated the feasibility of using this optofluidic system at different laboratories for bacterial identification. A global SERS-based dendrogram model for MRSA and MSSA identification and differentiation to the strain level was established and cross-validated (Simpson index of diversity of 0.989) and had an average recognition rate of 95% for S. aureus isolates associated with a recent outbreak in China. SERS typing correlated well with MLST indicating that it has high sensitivity and selectivity and would be suitable for determining the origin and possible spread of MRSA. A SERS-based partial least-squares regression model could quantify the actual concentration of a specific MRSA isolate in a bacterial mixture at levels from 5% to 100% (regression coefficient, >0.98; residual prediction deviation, >10.05). This optofluidic platform has advantages over traditional genotyping for ultrafast, automated, and reliable detection and epidemiological surveillance of bacterial infections.

Dataset Information

Inference and control of the nosocomial transmission of methicillin-resistant Staphylococcus aureus.

Publications

Inference and control of the nosocomial transmission of methicillin-resistant <i>Staphylococcus aureus</i>.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets