Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting

Characterization of Heterogeneous MRSA and MSSA with Reduced Susceptibility to Chlorhexidine in Kuwaiti Hospitals

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.

Emergence and Spread of Antimicrobial Resistance: Recent Insights from Bacterial Population Genomics

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.

MRSA Transmission Dynamics Among Interconnected Acute, Intermediate-Term, and Long-Term Healthcare Facilities in Singapore

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) is the most common healthcare-associated multidrug-resistant organism. Despite the interconnectedness between acute care hospitals (ACHs) and intermediate- and long-term care facilities (ILTCFs), the transmission dynamics of MRSA between healthcare settings is not well understood.

METHODS

We conducted a cross-sectional study in a network comprising an ACH and 5 closely affiliated ILTCFs in Singapore. A total of 1700 inpatients were screened for MRSA over a 6-week period in 2014. MRSA isolates underwent whole-genome sequencing, with a pairwise single-nucleotide polymorphism (Hamming distance) cutoff of 60 core genome single-nucleotide polymorphisms used to define recent transmission clusters (clades) for the 3 major clones.

RESULTS

MRSA prevalence was significantly higher in intermediate-term (29.9%) and long-term (20.4%) care facilities than in the ACH (11.8%) (P < .001). The predominant clones were sequence type [ST] 22 (n = 183; 47.8%), ST45 (n = 129; 33.7%), and ST239 (n = 26; 6.8%), with greater diversity of STs in ILTCFs relative to the ACH. A large proportion of the clades in ST22 (14 of 21 clades; 67%) and ST45 (7 of 13; 54%) included inpatients from the ACH and ILTCFs. The most frequent source of the interfacility transmissions was the ACH (n = 28 transmission events; 36.4%).

CONCLUSIONS

MRSA transmission dynamics between the ACH and ILTCFs were complex. The greater diversity of STs in ILTCFs suggests that the ecosystem in such settings might be more conducive for intrafacility transmission events. ST22 and ST45 have successfully established themselves in ILTCFs. The importance of interconnected infection prevention and control measures and strategies cannot be overemphasized.

Whole-Genome Sequencing Reveals the Contribution of Long-Term Carriers in Staphylococcus aureus Outbreak Investigation

Whole-genome sequencing (WGS) makes it possible to determine the relatedness of bacterial isolates at a high resolution, thereby helping to characterize outbreaks. However, for Staphylococcus aureus, the accumulation of within-host diversity during carriage might limit the interpretation of sequencing data. In this study, we hypothesized the converse, namely, that within-host diversity can in fact be exploited to reveal the involvement of long-term carriers (LTCs) in outbreaks. We analyzed WGS data from 20 historical outbreaks and applied phylogenetic methods to assess genetic relatedness and to estimate the time to most recent common ancestor (TMRCA). The findings were compared with the routine investigation results and epidemiological evidence. Outbreaks with epidemiological evidence for an LTC source had a mean estimated TMRCA (adjusted for outbreak duration) of 243 days (95% highest posterior density interval [HPD], 143 to 343 days) compared with 55 days (95% HPD, 28 to 81 days) for outbreaks lacking epidemiological evidence for an LTC (P = 0.004). A threshold of 156 days predicted LTC involvement with a sensitivity of 0.875 and a specificity of 1. We also found 6/20 outbreaks included isolates with differing antimicrobial susceptibility profiles; however, these had only modestly increased pairwise diversity (mean 17.5 single nucleotide variants [SNVs] [95% confidence interval {CI}, 17.3 to 17.8]) compared with isolates with identical antibiograms (12.7 SNVs [95% CI, 12.5 to 12.8]) (P < 0.0001). Additionally, for 2 outbreaks, WGS identified 1 or more isolates that were genetically distinct despite having the outbreak pulsed-field gel electrophoresis (PFGE) pulsotype. The duration-adjusted TMRCA allowed the involvement of LTCs in outbreaks to be identified and could be used to decide whether screening for long-term carriage (e.g., in health care workers) is warranted. Requiring identical antibiograms to trigger investigation could miss important contributors to outbreaks.

Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks

Genomic data are increasingly being used to understand infectious disease epidemiology. Isolates from a given outbreak are sequenced, and the patterns of shared variation are used to infer which isolates within the outbreak are most closely related to each other. Unfortunately, the phylogenetic trees typically used to represent this variation are not directly informative about who infected whom-a phylogenetic tree is not a transmission tree. However, a transmission tree can be inferred from a phylogeny while accounting for within-host genetic diversity by coloring the branches of a phylogeny according to which host those branches were in. Here we extend this approach and show that it can be applied to partially sampled and ongoing outbreaks. This requires computing the correct probability of an observed transmission tree and we herein demonstrate how to do this for a large class of epidemiological models. We also demonstrate how the branch coloring approach can incorporate a variable number of unique colors to represent unsampled intermediates in transmission chains. The resulting algorithm is a reversible jump Monte-Carlo Markov Chain, which we apply to both simulated data and real data from an outbreak of tuberculosis. By accounting for unsampled cases and an outbreak which may not have reached its end, our method is uniquely suited to use in a public health environment during real-time outbreak investigations. We implemented this transmission tree inference methodology in an R package called TransPhylo, which is freely available from https://github.com/xavierdidelot/TransPhylo.

Staphylococcus aureus biofilm: a complex developmental organism

Chronic biofilm-associated infections caused by Staphylococcus aureus often lead to significant increases in morbidity and mortality, particularly when associated with indwelling medical devices. This has triggered a great deal of research attempting to understand the molecular mechanisms that control S. aureus biofilm formation and the basis for the recalcitrance of these multicellular structures to antibiotic therapy. The purpose of this review is to summarize our current understanding of S. aureus biofilm development, focusing on the description of a newly-defined, five-stage model of biofilm development and the mechanisms required for each stage. Importantly, this model includes an alternate view of the processes involved in microcolony formation in S. aureus and suggests that these structures originate as a result of stochastically regulated metabolic heterogeneity and proliferation within a maturing biofilm population, rather than a subtractive process involving the release of cell clusters from a thick, unstructured biofilm. Importantly, it is proposed that this new model of biofilm development involves the genetically programmed generation of metabolically distinct subpopulations of cells, resulting in an overall population that is better able to adapt to rapidly changing environmental conditions.

Infection control in the new age of genomic epidemiology

With the growing importance of infectious diseases in health care and communicable disease outbreaks garnering increasing attention, new technologies are playing a greater role in helping us prevent health care-associated infections and provide optimal public health. The microbiology laboratory has always played a large role in infection control by providing tools to identify, characterize, and track pathogens. Recently, advances in DNA sequencing technology have ushered in a new era of genomic epidemiology, where traditional molecular diagnostics and genotyping methods are being enhanced and even replaced by genomics-based methods to aid epidemiologic investigations of communicable diseases. The ability to analyze and compare entire pathogen genomes has allowed for unprecedented resolution into how and why infectious diseases spread. As these genomics-based methods continue to improve in speed, cost, and accuracy, they will be increasingly used to inform and guide infection control and public health practices.

Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname

We report the investigation of an outbreak situation of methicillin-resistant Staphylococcus aureus (MRSA) that occurred at the Academic Hospital Paramaribo (AZP) in the Republic of Suriname from April to May 2013. We performed whole genome sequencing with complete gap closure for chromosomes and plasmids on all isolates. The outbreak involved 12 patients and 1 healthcare worker/nurse at the AZP. In total 24 isolates were investigated. spa typing, genome-wide single nucleotide polymorphism (SNP) analysis, ad hoc whole genome multilocus sequence typing (wgMLST), stable core genome MLST (cgMLST) and in silico PFGE were used to determine phylogenetic relatedness and to identify transmission. Whole-genome sequencing (WGS) showed that all isolates were members of genomic variants of the North American USA300 clone. However, WGS revealed a heterogeneous population structure of USA300 circulating at the AZP. We observed up to 8 SNPs or up to 5 alleles of difference by wgMLST when the isolates were recovered from different body sites of the same patient or if direct transmission between patients was most likely. This work describes the usefulness of complete genome sequencing of bacterial chromosomes and plasmids providing an unprecedented level of detail during outbreak investigations not being visible by using conventional typing methods.

Whole genome sequencing to investigate a putative outbreak of the virulent community-associated methicillin-resistant Staphylococcus aureus ST93 clone in a remote Indigenous community

We report two cases of severe pneumonia due to clone ST93 methicillin-resistant Staphylococcus aureus (MRSA) presenting from a remote Australian Indigenous community within a 2-week period, and the utilization of whole genome sequences to determine whether these were part of an outbreak. S. aureus was isolated from 12 of 92 nasal swabs collected from 25 community households (including the two index households); one isolate was ST93. Three of five skin lesion S. aureus isolates obtained at the community were ST93. Whole genome sequencing of the ST93 isolates from this study and a further 20 ST93 isolates from the same region suggested that recent transmission and progression to disease had not taken place. The proximity in time and space of the two severe pneumonia cases is probably a reflection of the high burden of disease due to ST93 MRSA in this population where skin infections and household crowding are common.

Transmission of Staphylococcus aureus between health-care workers, the environment, and patients in an intensive care unit: a longitudinal cohort study based on whole-genome sequencing

Background

Health-care workers have been implicated in nosocomial outbreaks of Staphylococcus aureus, but the dearth of evidence from non-outbreak situations means that routine health-care worker screening and S aureus eradication are controversial. We aimed to determine how often S aureus is transmitted from health-care workers or the environment to patients in an intensive care unit (ICU) and a high-dependency unit (HDU) where standard infection control measures were in place.

Methods

In this longitudinal cohort study, we systematically sampled health-care workers, the environment, and patients over 14 months at the ICU and HDU of the Royal Sussex County Hospital, Brighton, England. Nasal swabs were taken from health-care workers every 4 weeks, bed spaces were sampled monthly, and screening swabs were obtained from patients at admission to the ICU or HDU, weekly thereafter, and at discharge. Isolates were cultured and their whole genome sequenced, and we used the threshold of 40 single-nucleotide variants (SNVs) or fewer to define subtypes and infer recent transmission.

Findings

Between Oct 31, 2011, and Dec 23, 2012, we sampled 198 health-care workers, 40 environmental locations, and 1854 patients; 1819 isolates were sequenced. Median nasal carriage rate of S aureus in health-care workers at 4-weekly timepoints was 36·9% (IQR 35·7–37·3), and 115 (58%) health-care workers had S aureus detected at least once during the study. S aureus was identified in 8–50% of environmental samples. 605 genetically distinct subtypes were identified (median SNV difference 273, IQR 162–399) at a rate of 38 (IQR 34–42) per 4-weekly cycle. Only 25 instances of transmission to patients (seven from health-care workers, two from the environment, and 16 from other patients) were detected.

Interpretation

In the presence of standard infection control measures, health-care workers were infrequently sources of transmission to patients. S aureus epidemiology in the ICU and HDU is characterised by continuous ingress of distinct subtypes rather than transmission of genetically related strains.

Funding

UK Medical Research Council, Wellcome Trust, Biotechnology and Biological Sciences Research Council, UK National Institute for Health Research, and Public Health England.

Livestock-Associated Methicillin Resistant Staphylococcus aureus (LA-MRSA) Clonal Complex (CC) 398 Isolated from UK Animals belong to European Lineages

In recent years, there has been an increase in the number of livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 recovered from S. aureus isolated animals in the UK. To determine possible origins of 12 LA-MRSA CC398 isolates collected after screening more than a thousand S. aureus animal isolates from the UK between 2013 and 2015, whole genome sequences (WGS) of CC398 European, including UK, and non-European isolates from diverse animal hosts were compared. Phylogenetic reconstruction applied to WGS data to assess genetic relatedness of all 89 isolates, clustered the 12 UK CC398 LA-MRSA within the European sub-lineages, although on different nodes; implicating multiple independent incursions into the UK, as opposed to a single introduction followed by clonal expansion. Three UK isolates from healthy pigs and one from turkey clustered within the cassette chromosome recombinases ccr C S. aureus protein A (spa)-type t011 European sub-lineage and three UK isolates from horses within the ccrA2B2 t011 European sub-lineage. The remaining UK isolates, mostly from pigs, clustered within the t034 European lineage. Presence of virulence, antimicrobial (AMR), heavy metal (HMR), and disinfectant (DR) resistance genes were determined using an in-house pipeline. Most, including UK isolates, harbored resistance genes to ≥3 antimicrobial classes in addition to β-lactams. HMR genes were detected in most European ccrC positive isolates, with >80% harboring czrC, encoding zinc and cadmium resistance; in contrast ~60% ccrC isolates within non-European lineages and 6% ccrA2B2 isolates showed this characteristic. The UK turkey MRSA isolate did not harbor φAVβ avian prophage genes (SAAV_2008 and SAAV_2009) present in US MSSA isolates from turkey and pigs. Absence of some of the major human-associated MRSA toxigenic and virulence genes in the UK LA-MRSA animal isolates was not unexpected. Therefore, we can conclude that the 12 UK LA-MRSA isolates collected in the past 2 years most likely represent separate incursions into the UK from other European countries. The presence of zinc and cadmium resistance in all nine food animal isolates (pig and poultry), which was absent from the 3 horse isolates may suggest heavy metal use/exposure has a possible role in selection of some MRSA.

Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks

Background

Long-term care facilities (LTCF) are potential reservoirs for methicillin-resistant Staphylococcus aureus (MRSA), control of which may reduce MRSA transmission and infection elsewhere in the healthcare system. Whole-genome sequencing (WGS) has been used successfully to understand MRSA epidemiology and transmission in hospitals and has the potential to identify transmission between these and LTCF.

Methods

Two prospective observational studies of MRSA carriage were conducted in LTCF in England and Ireland. MRSA isolates were whole-genome sequenced and analyzed using established methods. Genomic data were available for MRSA isolated in the local healthcare systems (isolates submitted by hospitals and general practitioners).

Results

We sequenced a total of 181 MRSA isolates from the two study sites. The majority of MRSA were multilocus sequence type (ST)22. WGS identified one likely transmission event between residents in the English LTCF and three putative transmission events in the Irish LTCF. WGS also identified closely related isolates present in colonized Irish residents and their immediate environment. Based on phylogenetic reconstruction, closely related MRSA clades were identified between the LTCF and their healthcare referral network, together with putative MRSA acquisition by LTCF residents during hospital admission.

Conclusions

These data confirm that MRSA is transmitted between residents of LTCF and is both acquired and transmitted to others in referral hospitals and beyond. Our data present compelling evidence for the importance of environmental contamination in MRSA transmission, reinforcing the importance of environmental cleaning. The use of WGS in this study highlights the need to consider infection control in hospitals and community healthcare facilities as a continuum.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-016-0353-5) contains supplementary material, which is available to authorized users.

Genomics of Natural Populations of Staphylococcus aureus

Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. The first S. aureus genomes to be published, 15 years ago, provided the first view of genome structure and gene content. Since then, thousands of genomes from a wide array of strains from different sources have been sequenced. Comparison of these sequences has resulted in broad insights into population structure, bacterial evolution, clone emergence and expansion, and the molecular basis of niche adaptation. Furthermore, this information is now being applied clinically in outbreak investigations to inform infection control measures and to determine appropriate treatment regimens. In this review, we summarize some of the broad insights into S. aureus biology gained from the analysis of genomes and discuss future directions and opportunities in this dynamic field of research.

Whole genome sequencing reveals extensive community-level transmission of group A Streptococcus in remote communities

Impetigo is common in remote Indigenous children of northern Australia, with the primary driver in this context being Streptococcus pyogenes [or group A Streptococcus (GAS)]. To reduce the high burden of impetigo, the transmission dynamics of GAS must be more clearly elucidated. We performed whole genome sequencing on 31 GAS isolates collected in a single community from children in 11 households with ⩾2 GAS-infected children. We aimed to determine whether transmission was occurring principally within households or across the community. The 31 isolates were represented by nine multilocus sequence types and isolates within each sequence type differed from one another by only 0-3 single nucleotide polymorphisms. There was evidence of extensive transmission both within households and across the community. Our findings suggest that strategies to reduce the burden of impetigo in this setting will need to extend beyond individual households, and incorporate multi-faceted, community-wide approaches.

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement. Among these, AF methods are most sensitive to the extent of sequence divergence, less sensitive to low and moderate frequencies of LGT, and most robust against genome rearrangement. We describe the application of AF methods to three well-studied empirical genome datasets, and introduce a new application of the jackknife to assess node support. Our results demonstrate that AF phylogenomics is computationally scalable to multi-genome data and can generate biologically meaningful phylogenies and insights into microbial evolution.

Next-Generation Sequencing Confirms Presumed Nosocomial Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus in the Netherlands

Livestock-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.

IMPORTANCE

In 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.

New Is Old, and Old Is New: Recent Advances in Antibiotic-Based, Antibiotic-Free and Ethnomedical Treatments against Methicillin-Resistant Staphylococcus aureus Wound Infections

Staphylococcus aureus is the most common pathogen of wound infections. Thus far, methicillin-resistant S. aureus (MRSA) has become the major causative agent in wound infections, especially for nosocomial infections. MRSA infections are seldom eradicated by routine antimicrobial therapies. More concerning, some strains have become resistant to the newest antibiotics of last resort. Furthermore, horizontal transfer of a polymyxin resistance gene, mcr-1, has been identified in Enterobacteriaceae, by which resistance to the last group of antibiotics will likely spread rapidly. The worst-case scenario, "a return to the pre-antibiotic era", is likely in sight. A perpetual goal for antibiotic research is the discovery of an antibiotic that lacks resistance potential, such as the recent discovery of teixobactin. However, when considering the issue from an ecological and evolutionary standpoint, it is evident that it is insufficient to solve the antibiotic dilemma through the use of antibiotics themselves. In this review, we summarized recent advances in antibiotic-based, antibiotic-free and ethnomedical treatments against MRSA wound infections to identify new clues to solve the antibiotic dilemma. One potential solution is to use ethnomedical drugs topically. Some ethnomedical drugs have been demonstrated to be effective antimicrobials against MRSA. A decline in antibiotic resistance can therefore be expected, as has been demonstrated when antibiotic-free treatments were used to limit the use of antibiotics. It is also anticipated that these drugs will have low resistance potential, although there is only minimal evidence to support this claim to date. More clinical trials and animal tests should be conducted on this topic.

Within-host evolution of bacterial pathogens

Whole-genome sequencing has opened the way for investigating the dynamics and genomic evolution of bacterial pathogens during the colonization and infection of humans. The application of this technology to the longitudinal study of adaptation in an infected host--in particular, the evolution of drug resistance and host adaptation in patients who are chronically infected with opportunistic pathogens--has revealed remarkable patterns of convergent evolution, suggestive of an inherent repeatability of evolution. In this Review, we describe how these studies have advanced our understanding of the mechanisms and principles of within-host genome evolution, and we consider the consequences of findings such as a potent adaptive potential for pathogenicity. Finally, we discuss the possibility that genomics may be used in the future to predict the clinical progression of bacterial infections and to suggest the best option for treatment.

Carriage, Clinical Microbiology and Transmission of Staphylococcus aureus

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.

Genomic Epidemiology of USA300 Methicillin-Resistant Staphylococcus aureus in an Urban Community

BACKGROUND

In a community, it is unknown what factors account for transmission of methicillin-resistant Staphylococcus aureus (MRSA). We integrated whole genome sequencing (WGS) and epidemiologic data to identify factors associated with MRSA transmission networks in an urban community.

METHODS

WGS was performed on colonizing USA300 MRSA isolates from 74 individuals within 72 hours of admission to a public hospital in Chicago, IL. Single nucleotide variants (SNVs) were used to reconstruct the phylogeny of sequenced isolates, and epidemiologic data was overlaid to identify factors associated with transmission networks.

RESULTS

The maximum within-patient SNV difference for an individual with multisite colonization was 41 SNVs, with no systematic divergence among body sites. We observed a minimum of 7 SNVs and maximum of 153 SNVs between isolates from different individuals. We identified 4 pairs of individuals whose isolates were within 40 SNVs of each other. Putting our isolates in the context of previously sequenced USA300 isolates from other communities, we identified a 13-member group and two 4-member groups that represent samples from putative local transmission networks. Individuals in these groups were more likely to be African American, to be human immunodeficiency virus-infected, to reside in high detainee release areas, and to be current users of illicit drugs.

CONCLUSIONS

Using WGS, we observed potential transmission networks in an urban community and that certain epidemiologic factors were associated with inclusion in these networks. Future work with contact tracing and advanced molecular diagnostics may allow for identification of MRSA "epicenters" in the community where interventions can be targeted.

Genomic perspectives on the evolution and spread of bacterial pathogens

Since the first complete sequencing of a free-living organism, Haemophilus influenzae, genomics has been used to probe both the biology of bacterial pathogens and their evolution. Single-genome approaches provided information on the repertoire of virulence determinants and host-interaction factors, and, along with comparative analyses, allowed the proposal of hypotheses to explain the evolution of many of these traits. These analyses suggested many bacterial pathogens to be of relatively recent origin and identified genome degradation as a key aspect of host adaptation. The advent of very-high-throughput sequencing has allowed for detailed phylogenetic analysis of many important pathogens, revealing patterns of global and local spread, and recent evolution in response to pressure from therapeutics and the human immune system. Such analyses have shown that bacteria can evolve and transmit very rapidly, with emerging clones showing adaptation and global spread over years or decades. The resolution achieved with whole-genome sequencing has shown considerable benefits in clinical microbiology, enabling accurate outbreak tracking within hospitals and across continents. Continued large-scale sequencing promises many further insights into genetic determinants of drug resistance, virulence and transmission in bacterial pathogens.

A Retrospective Study on Genetic Heterogeneity within Treponema Strains: Subpopulations Are Genetically Distinct in a Limited Number of Positions

BACKGROUND

Pathogenic uncultivable treponemes comprise human and animal pathogens including agents of syphilis, yaws, bejel, pinta, and venereal spirochetosis in rabbits and hares. A set of 10 treponemal genome sequences including those of 4 Treponema pallidum ssp. pallidum (TPA) strains (Nichols, DAL-1, Mexico A, SS14), 4 T. p. ssp. pertenue (TPE) strains (CDC-2, Gauthier, Samoa D, Fribourg-Blanc), 1 T. p. ssp. endemicum (TEN) strain (Bosnia A) and one strain (Cuniculi A) of Treponema paraluisleporidarum ecovar Cuniculus (TPLC) were examined with respect to the presence of nucleotide intrastrain heterogeneous sites.

METHODOLOGY/PRINCIPAL FINDINGS

The number of identified intrastrain heterogeneous sites in individual genomes ranged between 0 and 7. Altogether, 23 intrastrain heterogeneous sites (in 17 genes) were found in 5 out of 10 investigated treponemal genomes including TPA strains Nichols (n = 5), DAL-1 (n = 4), and SS14 (n = 7), TPE strain Samoa D (n = 1), and TEN strain Bosnia A (n = 5). Although only one heterogeneous site was identified among 4 tested TPE strains, 16 such sites were identified among 4 TPA strains. Heterogeneous sites were mostly strain-specific and were identified in four tpr genes (tprC, GI, I, K), in genes involved in bacterial motility and chemotaxis (fliI, cheC-fliY), in genes involved in cell structure (murC), translation (prfA), general and DNA metabolism (putative SAM dependent methyltransferase, topA), and in seven hypothetical genes.

CONCLUSIONS/SIGNIFICANCE

Heterogeneous sites likely represent both the selection of adaptive changes during infection of the host as well as an ongoing diversifying evolutionary process.

Genome sequencing reveals strain dynamics of methicillin-resistant Staphylococcus aureus in the same household in the context of clinical disease in a person and a dog

The strain dynamics of methicillin-resistant Staphylococcus aureus (MRSA) isolates from people and the household dog were investigated. The isolates were identified in the context of a randomized controlled trial that tested household-wide decolonization of people. Genotypic comparison of MRSA isolates obtained from two household members, the dog, and home surfaces over a three-month period failed to implicate the pet or the home environment in recurrent colonization of the household members. However, it did implicate the pet's bed in exposure of the dog prior to the dog's infection. Whole genome sequencing was performed to differentiate the isolates. This report also describes introduction of diverse strains of MRSA into the household within six weeks of cessation of harmonized decolonization treatment of people and treatment for infection in the dog. These findings suggest that community sources outside the home may be important for recurrent MRSA colonization or infection.

Molecular Characterization of Staphylococcus aureus Isolates Transmitted between Patients with Buruli Ulcer

Background

Buruli ulcer (BU) is a skin infection caused by Mycobacterium ulcerans. The wounds of most BU patients are colonized with different microorganisms, including Staphylococcus aureus.

Methodology

This study investigated possible patient-to-patient transmission events of S. aureus during wound care in a health care center. S. aureus isolates from different BU patients with overlapping visits to the clinic were whole-genome sequenced and analyzed by a gene-by-gene approach using SeqSphere⁺ software. In addition, sequence data were screened for the presence of genes that conferred antibiotic resistance.

Principal Findings

SeqSphere⁺ analysis of whole-genome sequence data confirmed transmission of methicillin resistant S. aureus (MRSA) and methicillin susceptible S. aureus among patients that took place during wound care. Interestingly, our sequence data show that the investigated MRSA isolates carry a novel allele of the fexB gene conferring chloramphenicol resistance, which had thus far not been observed in S. aureus.

Buruli ulcer (BU) is a skin infection caused by Mycobacterium ulcerans. The wounds of most BU patients are colonized with different microorganisms, including Staphylococcus aureus. This study investigated patient-to-patient transmission events during wound care in a health care center. S. aureus isolates from patients who visited the health center at the same time points were analyzed using whole-genome sequencing. Analysis of sequence data confirmed transmission of methicillin resistant S. aureus and methicillin susceptible S. aureus among patients that took place during wound care.

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.

Whole-genome sequencing targets drug-resistant bacterial infections

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.

Within-host diversity of MRSA antimicrobial resistances

OBJECTIVES

MRSA is a major antimicrobial resistance (AMR) pathogen. The reservoir of infecting isolates is colonization, which is the site of evolutionary selection. The aim was to identify if AMRs in colonizing MRSA populations diversified and potential mechanisms of resistance gene transfer in vivo.

METHODS

Nasal swabs from 38 MRSA carriers admitted to hospital were plated and 20 individual colonies from each patient tested for phenotypic antibiotic susceptibility and genetically for lineage, carriage of four prophages and three plasmid families. Free bacteriophages were detected in swabs as well as their capacity for transducing resistance genes.

RESULTS

Nine (24%) patients carried phenotypic AMR variants and 24 (63%) carried prophage and plasmid variants. If a single colony was selected for testing, the probability of detecting all AMR in that patient was 87%. Sixty-four different AMR and mobile genetic element (MGE) profiles were detected, mostly in the MRSA CC22 background (where CC stands for clonal complex), with up to 8 profiles per patient. Nearly half of the patients carried detectable free bacteriophages and phages successfully transduced resistance genes between laboratory and patient isolates in vitro. WGS showed MRSA core genomes were stable, while AMR and MGEs varied.

CONCLUSIONS

'Clouds' of MRSA variants that have acquired or lost AMR and MGEs are common in nasal colonizing populations and bacteriophages may play an important role in gene transfer. Accurate estimation of AMR and genetic variability has implications for diagnostics, epidemiology, antimicrobial stewardship and understanding the evolutionary selection of AMR in colonizing populations.

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota

Bacterial whole genome sequencing holds promise as a disruptive technology in clinical microbiology, but it has not yet been applied systematically or comprehensively within a clinical context. Here, over the course of one year, we performed prospective collection and whole genome sequencing of nearly all bacterial isolates obtained from a tertiary care hospital's intensive care units (ICUs). This unbiased collection of 1,229 bacterial genomes from 391 patients enables detailed exploration of several features of clinical pathogens. A sizable fraction of isolates identified as clinically relevant corresponded to previously undescribed species: 12% of isolates assigned a species-level classification by conventional methods actually qualified as distinct, novel genomospecies on the basis of genomic similarity. Pan-genome analysis of the most frequently encountered pathogens in the collection revealed substantial variation in pan-genome size (1,420 to 20,432 genes) and the rate of gene discovery (1 to 152 genes per isolate sequenced). Surprisingly, although potential nosocomial transmission of actively surveilled pathogens was rare, 8.7% of isolates belonged to genomically related clonal lineages that were present among multiple patients, usually with overlapping hospital admissions, and were associated with clinically significant infection in 62% of patients from which they were recovered. Multi-patient clonal lineages were particularly evident in the neonatal care unit, where seven separate Staphylococcus epidermidis clonal lineages were identified, including one lineage associated with bacteremia in 5/9 neonates. Our study highlights key differences in the information made available by conventional microbiological practices versus whole genome sequencing, and motivates the further integration of microbial genome sequencing into routine clinical care.

Transmission of antimicrobial resistance in resource-poor healthcare

Inter-patient transfer of antimicrobial resistant pathogens is more common in resource-poor healthcare settings. In this age of global resistance, what contributes to the spread of antimicrobial resistant clones?