International travel as source of a hospital outbreak with an unusual meticillin-resistant Staphylococcus aureus clonal complex 398, Denmark, 2016

Emergence and control of an outbreak of PVL-positive MRSA in a UK-based maternity setting

This paper aims to describe the investigation and control of an outbreak of USA300 ST8 Panton-Valentine leucocidin (PVL)-positive meticillin-resistant Staphylococcus aureus (MRSA), confirmed by whole genome sequencing (WGS), within a maternity and neonatal setting in the UK. The identification of two linked PVL-MRSA cases led to an outbreak investigation. A lookback exercise conducted using the infection control surveillance database, typing of saved MRSA isolates, enhanced patient screening, and staff screening were used to identify further cases. Environmental screening was also performed. Genetic relatedness between isolates was assessed by WGS. During the outbreak, 18 cases were identified between 11th July 2021 and 22nd December 2022: 10 cases were infections and eight cases were colonizations. A healthcare worker (HCW) tested positive for colonization with the same strain, and environmental swabbing identified contaminated information technology equipment in the hospital. The outbreak was brought to an end by exclusion of the colonized HCW from work, and infection prevention and control measures. Since the end of the outbreak, cases of PVL-MRSA with similar molecular profiles have been found in the community. It is likely that the HCW played a role in the transmission of PVL-MRSA. Their exclusion from work and decolonization were key to preventing further cases. WGS was valuable in identifying and linking cases. The identification of community cases of PVL-MRSA with similar molecular profiles confirms transmission of the organism outside of healthcare settings.

A case of community-acquired Panton-Valentine leukocidin-positive methicillin-resistant Staphylococcus aureus (MRSA) necrotizing pneumonia successfully treated with two anti-MRSA drugs

A 22-year-old Vietnamese man was referred to our hospital owing to cough, dyspnea, and difficulty moving. The patient was diagnosed with community-acquired Panton-Valentine leukocidin-positive methicillin-resistant Staphylococcus aureus (MRSA) bacteremia and necrotizing pneumonia. Treatment involved vancomycin (VCM) and meropenem, and the MRSA bacteremia improved. However, lung tissue destruction progressed. Therefore, linezolid was added to the VCM regimen, and this intervention led to the patient's recovery, and he was discharged from the hospital. Here, we report a case in which the patient was treated with a combination of two anti-MRSA drugs and was cured.

Antibiotic resistance monitoring in wastewater in the Nordic countries: A systematic review

The Nordic countries (Denmark, Finland, Iceland, Norway, and Sweden) have effectively kept lower antibiotic-resistant bacterial (ARB) pathogen rates than many other countries. However, in recent years, these five countries have encountered a rise in ARB cases and challenges in treating infections due to the growing prevalence of ARB pathogens. Wastewater-based surveillance (WBS) is a valuable supplement to clinical methods for ARB surveillance, but there is a lack of comprehensive understanding of WBS application for ARB in the Nordic countries. This review aims to compile the latest state-of-the-art developments in WBS for ARB monitoring in the Nordic countries and compare them with clinical surveillance practices. After reviewing 1480 papers from the primary search, 54 were found relevant, and 15 additional WBS-related papers were included. Among 69 studies analyzed, 42 dedicated clinical epidemiology, while 27 focused on wastewater monitoring. The PRISMA review of the literature revealed that Nordic countries focus on four major WBS objectives of ARB: assessing ARB in the human population, identifying ARB evading wastewater treatment, quantifying removal rates, and evaluating potential ARB evolution during the treatment process. In both clinical and wastewater contexts, the most studied targets were pathogens producing carbapenemase and extended-spectrum beta-lactamase (ESBL), primarily Escherichia coli and Klebsiella spp. However, vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have received more attention in clinical epidemiology than in wastewater studies, probably due to their lower detection rates in wastewater. Clinical surveillance has mostly used culturing, antibiotic susceptibility testing, and genotyping, but WBS employed PCR-based and metagenomics alongside culture-based techniques. Imported cases resulting from international travel and hospitalization abroad appear to have frequently contributed to the rise in ARB pathogen cases in these countries. The many similarities between the Nordic countries (e.g., knowledge exchange practices, antibiotic usage patterns, and the current ARB landscape) could facilitate collaborative efforts in developing and implementing WBS for ARB in population-level screening.

A look at staphylococci from the one health perspective

Staphylococcus aureus and other staphylococcal species are resident and transient multihost colonizers as well as conditional pathogens. Especially S. aureus represents an excellent model bacterium for the "One Health" concept because of its dynamics at the human-animal interface and versatility with respect to host adaptation. The development of antimicrobial resistance plays another integral part. This overview will focus on studies at the human-animal interface with respect to livestock farming and to companion animals, as well as on staphylococci in wildlife. In this context transmissions of staphylococci and of antimicrobial resistance genes between animals and humans are of particular significance.

The Prevalence, Epidemiological, and Molecular Characterization of Methicillin-Resistant Staphylococcus aureus (MRSA) in Macau (2017-2022)

Macau, recognized as a global tourism hub and the world's most densely populated region, provides a unique environment conducive to methicillin-resistant Staphylococcus aureus (MRSA) transmission in healthcare and community settings, posing a significant public health concern both locally and globally. The epidemiology and molecular characteristics of MRSA in the distinct city of Macau remain largely unelucidated. This five-year longitudinal study (2017-2022) examined the local prevalence and molecular typing of MRSA in Macau, with future MRSA type distribution predicted through ARIMA modeling. We subsequently analyzed the epidemiological characteristics of MRSA, including specimen source, clinical department, collection year, season, patient age, sex, and the annual number of tourists. Comprehensive antibiotic resistance profiles of the strains were also assessed. Of 504 clinically isolated S. aureus strains, 183 (36.3%) were identified as MRSA by the cefoxitin disk diffusion method and validated through multi-locus sequence typing (MLST). The MRSA detection rate showed an upward trend, increasing from 30.1% in 2017 to 45.7% in 2022. SCCmec type IV was predominant (28.9%), followed by types II (25.4%), III (22.1%), and V (22.1%). The primary sources of MRSA isolates were sputum (39.2%) and secretions (25.6%). Older age emerged as a risk factor for MRSA infection, whereas no significant associations were found with seasonal variations, gender, or the annual number of tourists. Despite displaying universal resistance to cefoxitin, oxacillin, and benzylpenicillin, MRSA isolates in Macau remained fully sensitive to vancomycin, tigecycline, quinupristin, nitrofurantoin, and linezolid. Continuous surveillance and analysis of MRSA distribution in Macau could provide invaluable insights for the effective management of MRSA prevention and control measures within healthcare settings.

Whole-genome sequencing links cases dispersed in time, place, and person while supporting healthcare worker management in an outbreak of Panton-Valentine leucocidin meticillin-resistant Staphylococcus aureus; and a review of literature

This is a report on an outbreak of Panton-Valentine leucocidin-producing meticillin-resistant Staphylococcus aureus (PVL-MRSA) in an intensive care unit (ICU) during the COVID-19 pandemic that affected seven patients and a member of staff. Six patients were infected over a period of ten months on ICU by the same strain of PVL-MRSA, and a historic case identified outside of the ICU. All cases were linked to a healthcare worker (HCW) who was colonized with the organism. Failed topical decolonization therapy, without systemic antibiotic therapy, resulted in ongoing transmission and one preventable acquisition of PVL-MRSA. The outbreak identifies the support that may be needed for HCWs implicated in outbreaks. It also demonstrates the role of whole-genome sequencing in identifying dispersed and historic cases related to the outbreak, which in turn aids decision-making in outbreak management and HCW support. This report also includes a review of literature of PVL-MRSA-associated outbreaks in healthcare and highlights the need for review of current national guidance in the management of HCWs' decolonization regimen and return-to-work recommendations in such outbreaks.

The association between socioeconomic factors and the success of decolonization treatment among individuals diagnosed with methicillin-resistant Staphylococcus aureus: A cohort study from 2007 to 2020

OBJECTIVES

To examine associations between socioeconomic factors and (1) adherence to methicillin-resistant Staphylococcus aureus (MRSA) posttreatment follow-up swab sampling after 1 and 6 months and (2) successful decolonization treatment.

DESIGN

Cohort study with 2 years of follow-up. Data on patients diagnosed with MRSA were extracted from a regional MRSA database and national registries. We used a cluster-based logistic regression model to estimate the adjusted odds ratios (aOR) and 95% confidence interval (CI) for associations between socioeconomic factors and decolonization treatment.

SETTING

Danish primary health care.

RESULTS

The rate of adherence to posttreatment follow-up swab sampling among 2,536 cases 1 month after decolonization treatment was 66% (95% CI, 64%-68%), and it decreased to 30% (95% CI, 28%-32%) after 6 months. Living in intermediate municipalities (76-159 inhabitants/km2) or having retired were associated with completed posttreatment follow-up swabs 1 month after decolonization treatment: aOR, 1.40 (95% CI, 1.2-1.74) and aOR, 2.67 (95% CI, 1.16-6.13), respectively. The rate of successful decolonization treatment 2 years after initiating treatment was 36% (95% CI, 34%-38%). Factors associated with successful decolonization treatment included individuals with higher education (aOR, 1.62; 95% CI, 1.22-2.15), early retirees (aOR, 1.63; 95% CI, 1.12-2.38), those living in intermediate municipalities (ie, 160-900+ inhabitants/km2; aOR, 1.35; 95% CI, 1.08-1.68), and those living in predominantly urban municipalities (ie, 160-900+ inhabitants/km2; aOR, 2.04; 95% CI, 1.5-2.76).

CONCLUSIONS

Disparities in the effect of decolonization treatment and adherence to MRSA follow-up sampling among MRSA-positive individuals appear to be largely explained by the level of education, area of residence, and employment status.

Bacteremic necrotizing mediastinitis caused by community-associated clonal complex 398 methicillin-resistant Staphylococcus aureus in a baby aged 4 months

Invasive community-associated methicillin-resistant Staphylococcus aureus (MRSA) diseases caused by clonal complex 398 MRSA without animal contact have become a new emerging threat. We report a case of bacteremic mediastinitis caused by a Panton-Valentine leukocidin-positive community-associated sequence type 1232 MRSA in a Taiwanese baby aged 4 months without animal contact.

Livestock-associated methicillin-resistant Staphylococcus aureus epidemiology, genetic diversity, and clinical characteristics in an urban region

Objectives

While Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA), defined as CC398, is a well-known pathogen among those working with livestock, there are indications that LA-MRSA prevalence among the general population is increasing. However, the clinical impact in urban areas remains unknown. The aim of this study was to assess the genetic epidemiology and clinical characteristics of LA-MRSA in an urban area with a limited livestock population.

Methods

In this retrospective study, we evaluated LA-MRSA strains that were collected between 2014 and 2018 from patients who received clinical care in a single urban area in Netherlands. Patient files were assessed for livestock exposure data, clinical findings, and contact tracing information. Next-generation sequencing (NGS) analysis in combination with wgMLST was conducted to assess genetic diversity and relatedness and to detect virulence and resistance genes.

Results

LA-MRSA strains were cultured from 81 patients, comprising 12% of all the MRSA strains found in seven study laboratories between 2014 and 2018. No livestock link was found in 76% of patients (n = 61), and 28% of patients (n = 23) had an infection, mostly of the skin or soft tissue. Contact tracing had been initiated in 14 cases, leading to the identification of two hospital transmissions: a cluster of 9 cases and one of 2 cases. NGS data were available for 91% (n = 75) of the patients. wgMLST confirmed the clusters detected via contact tracing (n = 2) and identified 5 additional clusters without a known epidemiological link. Relevant resistance and virulence findings included the PVL virulence gene (3 isolates) and tetracycline resistance (79 isolates).

Conclusion

LA-MRSA may cause a relevant burden of disease in urban areas. Surprisingly, most infections in the present study occurred in the absence of a livestock link, suggesting inter-human transmission. These findings and the presence of PVL and other immune evasive complex virulence genes warrant future surveillance and preventative measures.

Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases

Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.

Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA

Mobile genetic elements (MGEs) are agents of horizontal gene transfer in bacteria, but can also be vertically inherited by daughter cells. Establishing the dynamics that led to contemporary patterns of MGEs in bacterial genomes is central to predicting the emergence and evolution of novel and resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex (CC) 398 is the dominant MRSA in European livestock and a growing cause of human infections. Previous studies have identified three categories of MGEs whose presence or absence distinguishes livestock-associated CC398 from a closely related and less antibiotic-resistant human-associated population. Here, we fully characterise the evolutionary dynamics of these MGEs using a collection of 1180 CC398 genomes, sampled from livestock and humans, over 27 years. We find that the emergence of livestock-associated CC398 coincided with the acquisition of a Tn916 transposon carrying a tetracycline resistance gene, which has been stably inherited for 57 years. This was followed by the acquisition of a type V SCCmec that carries methicillin, tetracycline, and heavy metal resistance genes, which has been maintained for 35 years, with occasional truncations and replacements with type IV SCCmec. In contrast, a class of prophages that carry a human immune evasion gene cluster and that are largely absent from livestock-associated CC398 have been repeatedly gained and lost in both human- and livestock-associated CC398. These contrasting dynamics mean that when livestock-associated MRSA is transmitted to humans, adaptation to the human host outpaces loss of antibiotic resistance. In addition, the stable inheritance of resistance-associated MGEs suggests that the impact of ongoing reductions in antibiotic and zinc oxide use in European farms on livestock-associated MRSA will be slow to be realised.

Genomic Characterisation of CC398 MRSA Causing Severe Disease in Australia

Complex (CC) 398 livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has been reported worldwide in a variety of food-animal species. Although CC398 is synonymous with LA-MRSA, community-associated MRSA (CA-MRSA) variants have emerged, including the Panton-Valentine leukocidin (PVL)-positive ST398-V and ST398 single locus variant ST1232-V, and the PVL-negative ST398-V clones. Using comparative genomic analysis, we determined if ten CC398 MRSA bacteraemia episodes recently identified in Australia were due to LA-MRSA or CA-MRSA CC398. The isolates were sourced from the Australian Group on Antimicrobial Resistance S. aureus surveillance program and episodes occurred across Australia Whole genome sequencing and phylogenetic comparison of the ten CC398 bacteraemia isolates with previously published CC398 MRSA whole-genome sequences identified the Australian CC398 isolates were closely related to the human-associated II-GOI clade, and the livestock-associated IIa clade. The identified CC398 MRSA clones were: PVL-positive ST1232-V (5C2&5), PVL-negative community-associated ST398-V (5C2&5) and livestock-associated ST398-V (5C2&5). Our findings demonstrate the importance of using whole genome sequencing and comparing the sequences to international sequences to distinguish between CC398 CA- and LA- MRSA and to determine the isolates' origin. Furthermore, our findings suggest CC398 CA-MRSA has become established in the Australian community and ST398-V (5C2&5) LA-MRSA is now widespread in Australian piggeries. Our study emphasizes the need of national one health antimicrobial resistance surveillance programs to assist in monitoring the ongoing epidemiology of MRSA and other clinically significant antimicrobial resistant organisms.

A Survey of Chinese Pig Farms and Human Healthcare Isolates Reveals Separate Human and Animal Methicillin-Resistant Staphylococcus aureus Populations

There has been increasing concern that the overuse of antibiotics in livestock farming is contributing to the burden of antimicrobial resistance in people. Farmed animals in Europe and North America, particularly pigs, provide a reservoir for livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA ST398 lineage) found in people. This study is designed to investigate the contribution of MRSA from Chinese pig farms to human infection. A collection of 483 MRSA are isolated from 55 farms and 4 hospitals in central China, a high pig farming density area. CC9 MRSA accounts for 97.2% of all farm isolates, but is not present in hospital isolates. ST398 isolates are found on farms and hospitals, but none of them formed part of the "LA-MRSA ST398 lineage" present in Europe and North America. The hospital ST398 MRSA isolate form a clade that is clearly separate from the farm ST398 isolates. Despite the presence of high levels of MRSA found on Chinese pig farms, the authors find no evidence of them spilling over to the human population. Nevertheless, the ST398 MRSA obtained from hospitals appear to be part of a widely distributed lineage in China. The new animal-adapted ST398 lineage that has emerged in China is of concern.

NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology

Hospital outbreak investigations are high-stakes epidemiology. Contacts between staff and patients are numerous; environmental and community exposures are plentiful; and patients are highly vulnerable. Having the best data is paramount to understanding an outbreak in order to stop ongoing transmission and prevent future outbreaks. In the past 5 years, the high-resolution view of transmission offered by analyzing pathogen whole-genome sequencing (WGS) is increasingly part of hospital outbreak investigations. Concerns over speed and actionability, assay validation, liability, cost, and payment models lead to further opportunities for work in this area. Now accelerated by funding for COVID-19, the use of genomics in hospital outbreak investigations has firmly moved from the academic literature to more quotidian operations, with associated concerns involving regulatory affairs, data integration, and clinical interpretation. This review details past uses of WGS data in hospital-acquired infection outbreaks as well as future opportunities to increase its utility and growth in hospital infection prevention.

Lateral Flow Immunoassay for the Detection of Panton-Valentine Leukocidin in Staphylococcus aureus From Skin and Soft Tissue Infections in the United Arab Emirates

Introduction

Panton Valentine leukocidin (PVL) is a virulence factor which is associated with methicillin sensitive and resistant Staphylococcus aureus (MSSA/MRSA) causing skin and soft tissue infections (SSTI). This study aimed to evaluate a novel lateral flow immunoassay (LFI) for PVL detection in S. aureus cultures and to describe their genotypic characterization.

Methods

The study was carried out from January-August 2020 in Dubai, United Arab Emirates. S. aureus isolates associated with SSTI were tested for PVL detection using LFI. DNA microarray-based assays were used for molecular characterization including detection of pvl genes.

Results

One-hundred thirty-five patients with a clinical diagnosis of SSTIs were recruited. Sixty-six patients received antibiotics, mostly beta lactams (n=36) and topical fusidic acid (n=15). One-hundred twenty-nine isolates (MRSA: n=43; MSSA: n=86) were tested by LFI and DNA microarrays. All 76 (58.9%) isolates which were unambiguously negative for the PVL in LFI were negative for pvl genes using the DNA microarray. All the LFI PVL positive isolates (n=53) had pvl genes detected. This translates into 100% each for sensitivity, specificity, positive and negative predictive values for the LFI. The LFI typically takes about 15 min inclusive of a 10 min incubation period. Predominant S. aureus clonal complexes (CC) were CC30 (n=18), CC22 (n=13), CC5 (n=12), CC1 (n=11), CC152 (n=8), CC15 (n=7); CC97 (n=7); CC8 and CC20 (n=6 each). Among MRSA, the proportion of pvl-positives (35/43; 81%) was higher than among MSSA (n/N=18/86; 21%). The fusidic acid resistance gene fusC was detected in 14 MRSA (33%) compared to 8 MSSA (9%). A co-carriage of fusC and pvl genes was present in 7 MRSA and in one MSSA.

Conclusion

LFI shows excellent diagnostic accuracy indices for rapid identification of PVL in MSSA/MRSA in a setting with high prevalence of pvl^+ve strains. The high occurrence of pvl and fusC genes in MRSA strains causing SSTI is of concern and needs constant surveillance.

Genotyping of methicillin resistant Staphylococcus aureus from the United Arab Emirates

Reports from Arabian Gulf countries have demonstrated emergence of novel methicillin resistant Staphylococcus aureus (MRSA) strains. To address the lack of data from the United Arab Emirates (UAE), genetic characterisation of MRSA identified between December 2017 and August 2019 was conducted using DNA microarray-based assays. The 625 MRSA isolates studied were grouped into 23 clonal complexes (CCs) and assigned to 103 strains. CC5, CC6, CC22 and CC30 represented 54.2% (n/N = 339/625) of isolates with other common CCs being CC1, CC8, CC772, CC361, CC80, CC88. Emergence of CC398 MRSA, CC5-MRSA-IV Sri Lanka Clone and ST5/ST225-MRSA-II, Rhine-Hesse EMRSA/New York-Japan Clone in our setting was detected. Variants of pandemic CC8-MRSA-[IVa + ACME I] (PVL+) USA300 were detected and majority of CC772 strains were CC772-MRSA-V (PVL+), “Bengal- Bay Clone”. Novel MRSA strains identified include CC5-MRSA-V (edinA+), CC5-MRSA-[VT + fusC], CC5-MRSA-IVa (tst1+), CC5-MRSA-[V/VT + cas + fusC + ccrA/B-1], CC8-MRSA-V/VT, CC22-MRSA-[IV + fusC + ccrAA/(C)], CC45-MRSA-[IV + fusC + tir], CC80-MRSA-IVa, CC121-MRSA-V/VT, CC152-MRSA-[V + fusC] (PVL+). Although several strains harboured SCC-borne fusidic acid resistance (fusC) (n = 181), erythromycin/clindamycin resistance (ermC) (n = 132) and gentamicin resistance (aacA-aphD) (n = 179) genes, none harboured vancomycin resistance genes while mupirocin resistance gene mupR (n = 2) and cfr gene (n = 1) were rare. An extensive MRSA repertoire including CCs previously unreported in the region and novel strains which probably arose locally suggest an evolving MRSA landscape.