Comprehensive modeling reveals proximity, seasonality, and hygiene practices as key determinants of MRSA colonization in exposed households

Bacterial Genotype, Carrier Risk Factors, and an Antimicrobial Stewardship Approach Relevant To Methicillin-resistant Staphylococcus Aureus Prevalence in a Population of Macaques Housed in a Research Facility

Methicillin-resistant Staphylococcus aureus (MRSA) remains a significant problem for human and animal health and can negatively affect the health status of macaques and other nonhuman primates (NHP) in research colonies. However, few publications provide guidance on the prevalence, genotype, or risk factors for macaques with MRSA and even fewer on how to effectively respond to MRSA once identified in a population. After having a clinical case of MRSA in a rhesus macaque, we sought to determine the MRSA carrier prevalence, risk factors, and genotypes of MRSA in a population of research NHPs. Over a 6-wk period in 2015, we collected nasal swabs from 298 NHPs. MRSA was isolated from 28% (n = 83). We then reviewed each macaque's medical record for a variety of variables including animal housing room, sex, age, number of antibiotic courses, number of surgical interventions, and SIV status. Analysis of these data suggests that MRSA carriage is associated with the room location, age of the animal, SIV status, and the number of antibiotic courses. We used multilocus sequence typing and spa typing on a subset of MRSA and MSSA isolates to determine whether the MRSA present in NHPs was comparable with common human strains. Two MRSA sequence types were predominant: ST188 and a novel MRSA genotype, neither of which is a common human isolate in the United States. We subsequently implemented antimicrobial stewardship practices (significantly reducing antimicrobial use) and then resampled the colony in 2018 and found that MRSA carriage had fallen to 9% (26/285). These data suggest that, as in humans, macaques may have a high carrier status of MRSA despite low clinically apparent disease. Implementing strategic antimicrobial stewardship practices resulted in a marked reduction in MRSA carriage in the NHP colony, highlighting the importance of limiting antimicrobial use when possible.

Effect of climate on surgical site infections and anticipated increases in the United States

Surgical site infections (SSI) are one of the most common and costly hospital-acquired infections in the United States. Meteorological variables such as temperature, humidity, and precipitation may represent a neglected group of risk factors for SSI. Using a national private insurance database, we collected admission and follow-up records for National Healthcare Safety Network-monitored surgical procedures and associated climate conditions from 2007 to 2014. We found that every 10 cm increase of maximum daily precipitation resulted in a 1.09 odds increase in SSI after discharge, while every g/kg unit increase in specific humidity resulted in a 1.03 odds increase in SSI risk after discharge. We identified the Southeast region of the United States at highest risk of climate change-related SSI, with an estimated 3% increase in SSI by 2060 under high emission assumptions. Our results describe the effect of climate on SSI and the potential burden of climate-change related SSI in the United States.

Changes in molecular characteristics and antimicrobial resistance of invasive Staphylococcus aureus infection strains isolated from children in Kunming, China during the COVID-19 epidemic

Invasive Staphylococcus aureus (S. aureus) infection is associated with high rates of mortality in children. No studies have been reported on invasive S. aureus infection among children in Kunming, China, and it remains unknown whether the COVID-19 epidemic has affected S. aureus prevalence in this region. Thus, this study investigated the changes in molecular characteristics and antimicrobial resistance of invasive S. aureus strains isolated from children in Kunming during 2019–2021. In total, 66 invasive S. aureus strains isolated from children were typed by multilocus sequence typing (MLST), spa, and Staphylococcal cassette chromosome mec (SCCmec), and antimicrobial resistance and virulence genes were analyzed. A total of 19 ST types, 31 spa types and 3 SCCmec types were identified. Thirty nine (59.09%) strains were methicillin-sensitive S. aureus (MSSA) and 27 (40.91%) strains were methicillin-resistant S. aureus (MRSA). The most common molecular type was ST22-t309 (22.73%, 15/66), followed by ST59-t437 (13.64%, 9/66). In 2019 and 2021, the dominant molecular type was ST22-t309, while in 2020, it was ST59-t437. After 2019, the dominant molecular type of MRSA changed from ST338-t437 to ST59-t437. All strains were susceptible to tigecycline, ciprofloxacin, moxifloxacin, vancomycin, quinopudine-dafoputin, linezolid, levofloxacin, and rifampicin. From 2019 to 2021, the resistance to penicillin and sulfamethoxazole initially decreased and then increased, a trend that contrasted with the observed resistance to oxacillin, cefoxitin, erythromycin, clindamycin, and tetracycline. Sixteen antimicrobial resistance profiles were identified, with penicillin-tetracycline-erythromycin-clindamycin-oxacillin-cefoxitin being the most common, and the antimicrobial resistance profiles varied by year. The carrier rates of virulence genes, icaA, icaD, hla, fnbA, fnbB, clfA, clfB, and cna were 100.00%. Furthermore, sak, pvl, icaC, icaR, fib, lip, hlb, hysA, sea, seb, and tsst-1 had carrier rates of 96.97, 92.42, 87.88, 69.70, 84.85, 62.12, 56.06, 50, 37.87, 30.30, and 7.58%, respectively. Since COVID-19 epidemic, the annual number of invasive S. aureus strains isolated from children in Kunming remained stable, but the molecular characteristics and antimicrobial resistance profiles of prevalent S. aureus strains have changed significantly. Thus, COVID-19 prevention and control should be supplemented by surveillance of common clinical pathogens, particularly vigilance against the prevalence of multidrug-resistant and high-virulence strains.

Transmission routes of antibiotic resistant bacteria: a systematic review

Background

Quantification of acquisition routes of antibiotic resistant bacteria (ARB) is pivotal for understanding transmission dynamics and designing cost-effective interventions. Different methods have been used to quantify the importance of transmission routes, such as relative risks, odds ratios (OR), genomic comparisons and basic reproduction numbers. We systematically reviewed reported estimates on acquisition routes’ contributions of ARB in humans, animals, water and the environment and assessed the methods used to quantify the importance of transmission routes.

Methods

PubMed and EMBASE were searched, resulting in 6054 articles published up until January 1st, 2019. Full text screening was performed on 525 articles and 277 are included.

Results

We extracted 718 estimates with S. aureus (n = 273), E. coli (n = 157) and Enterobacteriaceae (n = 99) being studied most frequently. Most estimates were derived from statistical methods (n = 560), mainly expressed as risks (n = 246) and ORs (n = 239), followed by genetic comparisons (n = 85), modelling (n = 62) and dosage of ARB ingested (n = 17). Transmission routes analysed most frequently were occupational exposure (n = 157), travelling (n = 110) and contacts with carriers (n = 83). Studies were mostly performed in the United States (n = 142), the Netherlands (n = 87) and Germany (n = 60). Comparison of methods was not possible as studies using different methods to estimate the same route were lacking. Due to study heterogeneity not all estimates by the same method could be pooled.

Conclusion

Despite an abundance of published data the relative importance of transmission routes of ARB has not been accurately quantified. Links between exposure and acquisition are often present, but the frequency of exposure is missing, which disables estimation of transmission routes’ importance. To create effective policies reducing ARB, estimates of transmission should be weighed by the frequency of exposure occurrence.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07360-z.

Longitudinal Dynamics of Skin Bacterial Communities in the Context of Staphylococcus aureus Decolonization

Decolonization with topical antimicrobials is frequently prescribed in health care and community settings to prevent Staphylococcus aureus infection. However, effects on commensal skin microbial communities remains largely unexplored. Within a household affected by recurrent methicillin-resistant S. aureus skin and soft tissue infections (SSTI), skin swabs were collected from the anterior nares, axillae, and inguinal folds of 14 participants at 1- to 3-month intervals over 24 months. Four household members experienced SSTI during the first 12-months (observational period) and were prescribed a 5-day decolonization regimen with intranasal mupirocin and bleach water baths at the 12-month study visit. We sequenced the 16S rRNA gene V1-V2 region and compared bacterial community characteristics between the pre- and post-intervention periods and between younger and older subjects. The median Shannon diversity index was stable during the 12-month observational period at all three body sites. Bacterial community characteristics (diversity, stability, and taxonomic composition) varied with age. Among all household members, not exclusively among the four performing decolonization, diversity was unstable throughout the year post-intervention. In the month after decolonization, bacterial communities were changed. Although communities largely returned to their baseline states, relative abundance of some taxa remained changed throughout the year following decolonization (e.g., more abundant Bacillus; less abundant Cutibacterium). This 5-day decolonization regimen caused disruption of skin bacteria, and effects differed in younger and older subjects. Some effects were observed throughout the year post-intervention, which emphasizes the need for better understanding of the collateral effects of decolonization for S. aureus eradication. IMPORTANCE Decolonization with topical antimicrobials is frequently prescribed to prevent Staphylococcus aureus infection, but the effects on commensal skin bacteria are undetermined. We found that decolonization with mupirocin and bleach water baths leads to sustained disruption of bacterial communities.

Management and Prevention of Staphylococcus aureus Infections in Children

Staphylococcus aureus is a common skin commensal with the potential to cause severe infections resulting in significant morbidity and mortality. Up to 30% of individuals are colonized with S aureus, though infection typically does not occur without skin barrier disruption. Infection management includes promptly addressing the source of infection, including sites of metastatic infection, and initiation of effective antibiotics, which should be selected based on local antibiotic susceptibility patterns. Given that S aureus colonization is a risk factor for infection, preventive strategies are aimed at optimizing hygiene measures and decolonization regimens for outpatients and critically ill children with prolonged hospitalizations.

Early development of the skin microbiome: therapeutic opportunities

As human skin hosts a diverse microbiota in health and disease, there is an emerging consensus that dysregulated interactions between host and microbiome may contribute to chronic inflammatory disease of the skin. Neonatal skin is a unique habitat, structurally similar to the adult but with a different profile of metabolic substrates, environmental stressors, and immune activity. The surface is colonized within moments of birth with a bias toward maternal strains. Initial colonists are outcompeted as environmental exposures increase and host skin matures. Nonetheless, early life microbial acquisitions may have long-lasting effects on health through modulation of host immunity and competitive interactions between bacteria. Microbial ecology and its influence on health have been of interest to dermatologists for >50 years, and an explosion of recent interest in the microbiome has prompted ongoing investigations of several microbial therapeutics for dermatological disease. In this review, we consider how recent insight into the host and microbial factors driving development of the skin microbiome in early life offers new opportunities for therapeutic intervention. IMPACT: Advancement in understanding molecular mechanisms of bacterial competition opens new avenues of investigation into dermatological disease. Primary development of the skin microbiome is determined by immunological features of the cutaneous habitat. Understanding coordinated microbial and immunological development in the pediatric patient requires a multidisciplinary synthesis of primary literature.

The Indirect Impact of the SARS-CoV-2 Pandemic on Invasive Group a Streptococcus, Streptococcus Pneumoniae and Staphylococcus Aureus Infections in Houston Area Children

Masking and social distancing have been adopted to mitigate the severe acute respiratory syndrome coronavirus 2 pandemic. We evaluated the indirect impact of severe acute respiratory syndrome coronavirus 2 prevention strategies on invasive Staphylococcus aureus, Streptococcus pneumoniae (pneumococcus) and Group A Streptococcus in Houston area children. We observed a decline in invasive pneumococcal disease and invasive Group A Streptococcus temporally associated with social distancing/masking/school closures.

Antibiotic Resistance Pattern of Staphylococcus Aureus Isolated From Pediatrics With Ocular Infections: A 6-Year Hospital-Based Study in China

Staphylococcus aureus (S. aureus) is an important pathogen of ocular infections in pediatrics. The study aimed to identify the prevalence and resistance pattern of S. aureus, especially methicillin-resistant S. aureus (MRSA), in Chinese children with ocular infections. All patients with S. aureus infections were reviewed at a tertiary children's hospital during 2015-2020, and those with ocular infections were investigated for susceptibility results. Of 1,668 S. aureus strains, there were 177 unique isolates from ocular infection. Among them, 45 (25.4%) were MRSA and 132 (74.6%) were methicillin-sensitive S. aureus (MSSA). The proportion of MRSA did not change over time. Most of the strains were obtained from the neonate ward and ophthalmology department (n = 88, 49.7%, and n = 85, 48.0%, respectively), while eye secretion and pus were the main specimen types (n = 128, 72.3%, and n = 37, 20.9%, respectively). MRSA was significantly resistant against penicillin class (97.8%), erythromycin (71.1%), clindamycin (71.1%), and tetracycline (32.1%), with a high multidrug resistance (MDR) rate of 71.1%. However, MRSA was highly sensitive to levofloxacin. Resistance rates against erythromycin and ciprofloxacin as well as MDR percentage all increased among MSSA in children above 1 year of age, ophthalmology department, and outpatient population and decreased in eye secretion specimen. The mean resistance percentage remained stable for MRSA and MSSA during the study period. The survey of ocular S. aureus pathogens in pediatrics and their antibiotic resistance patterns helps in clinical treatment. MRSA with many strains demonstrating MDR is highly prevalent in children with ocular infections in Southeast China. Levofloxacin is an effective topical antibiotic for ocular MRSA infection, while erythromycin has a high resistance rate. The antibiotic resistance patterns of MRSA and MSSA differs and varies by different stratifications. A cautious use of antibiotics should be considered.

HOME2: Household vs. Personalized Decolonization in Households of Children with Methicillin-Resistant Staphylococcus aureus Skin and Soft Tissue Infection - A Randomized Clinical Trial

BACKGROUND

A household approach to decolonization decreases skin and soft tissue infection (SSTI) incidence, though this is burdensome and costly. As prior SSTI increases risk for SSTI, we hypothesized the effectiveness of decolonization measures to prevent SSTI when targeted to household members with prior year SSTI would be non-inferior to decolonizing all household members.

METHODS

Upon completion of our 12-month observational HOME study, 102 households were enrolled in HOME2, a 12-month, randomized non-inferiority trial. Pediatric index patients with community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) SSTI, their household contacts, and pets were enrolled. Households were randomized 1:1 to the Personalized (decolonization performed only by household members who experienced SSTI during the HOME study) or Household (decolonization performed by all household members) approaches. The 5-day regimen included hygiene education, twice-daily intranasal mupirocin, and daily bleach-water baths. At 5 follow-up visits in participants' homes, swabs to detect S. aureus were collected from participants, environmental surfaces, and pets; incident SSTI were ascertained.

RESULTS

Non-inferiority of the Personalized Approach was established for the primary outcome 3-month cumulative SSTI: 23 of 212 (10.8%) participants reported SSTI in Household Approach households, while 23 of 236 (9.7%) participants reported SSTI in Personalized Approach households; difference in proportions -1.1% (95% CI -6.7%, 4.5%). In multivariable analyses, prior year SSTI and baseline MRSA colonization were associated with cumulative SSTI.

CONCLUSIONS

The Personalized Approach was non-inferior to the Household Approach in preventing SSTI. Future studies should interrogate longer durations of decolonization and/or decontamination of the household environment to reduce household MRSA burden.

Environmental Methicillin-resistant Staphylococcus aureus Contamination, Persistent Colonization, and Subsequent Skin and Soft Tissue Infection

IMPORTANCE

The longitudinal association among persistent Staphylococcus aureus colonization, household environmental contamination, and recurrent skin and soft tissue infection (SSTI) is largely unexplored to date.

OBJECTIVES

To identify factors associated with persistent S aureus colonization and recurrent SSTI in households with children with community-associated methicillin-resistant S aureus (MRSA) SSTI.

DESIGN, SETTING, AND PARTICIPANTS

This 12-month prospective cohort study included 150 children with community-associated MRSA SSTI, 542 household contacts, and 154 pets enrolled from January 3, 2012, through October 20, 2015. A total of 5 quarterly home visits were made to 150 households in the St Louis, Missouri, region. Statistical analysis was performed from September 18, 2018, to January 7, 2020.

EXPOSURES

Covariates used in S aureus strain persistence and interval SSTI models included S aureus colonization and contamination measures, personal hygiene and sharing habits, health history, activities external to the home, and household characteristics (eg, cleanliness, crowding, home ownership, and pets). Serial samples to detect S aureus were collected from household members at 3 anatomic sites, from pets at 2 anatomic sites, and from environmental surfaces at 21 sites.

MAIN OUTCOMES AND MEASURES

Molecular epidemiologic findings of S aureus isolates were assessed via repetitive-sequence polymerase chain reaction. Individual persistent colonization was defined as colonization by an identical strain for 2 consecutive samplings. Longitudinal, multivariable generalized mixed-effects logistic regression models were used to assess factors associated with persistent S aureus personal colonization, environmental contamination, and interval SSTI.

RESULTS

Among 692 household members in 150 households, 326 (47%) were male and 366 (53%) were female, with a median age of 14.82 years (range, 0.05-82.25 years). Of 540 participants completing all 5 samplings, 213 (39%) were persistently colonized with S aureus, most often in the nares and with the strain infecting the index patient at enrollment. Nine pets (8%) were persistently colonized with S aureus. Participants reporting interval intranasal mupirocin application were less likely to experience persistent colonization (odds ratio [OR], 0.44; 95% credible interval [CrI], 0.30-0.66), whereas increasing strain-specific environmental contamination pressure was associated with increased individual persistent colonization (OR, 1.17; 95% CrI, 1.06-1.30). Strains with higher colonization pressure (OR, 1.47; 95% CrI, 1.25-1.71) and MRSA strains (OR, 1.57; 95% CrI, 1.16-2.19) were more likely to persist. Seventy-six index patients (53%) and 101 household contacts (19%) reported interval SSTIs. Individuals persistently colonized with MRSA (OR, 1.56; 95% CrI, 1.17-2.11), those with a history of SSTI (OR, 2.55; 95% CrI, 1.88-3.47), and index patients (OR, 1.54; 95% CrI, 1.07-2.23) were more likely to report an interval SSTI.

CONCLUSIONS AND RELEVANCE

The study findings suggest that recurrent SSTI is associated with persistent MRSA colonization of household members and contamination of environmental surfaces. Future studies may elucidate the effectiveness of specific combinations of personal decolonization and environmental decontamination efforts in eradicating persistent strains and mitigating recurrent SSTIs.

Changing epidemiology of methicillin-resistant Staphylococcus aureus in a low endemicity area-new challenges for MRSA control

The incidence of methicillin-resistant Staphylococcus aureus (MRSA) has increased sharply in Hospital District of Southwest Finland (HD). To understand reasons behind this, a retrospective, population-based study covering 10 years was conducted. All new 983 MRSA cases in HD from January 2007 to December 2016 were analysed. Several data sources were used to gather background information on the cases. MRSA cases were classified as healthcare-associated (HA-MRSA), community-associated (CA-MRSA), and livestock contact was determined (livestock-associated MRSA, LA-MRSA). Spa typing was performed to all available strains. The incidence of MRSA doubled from 12.4 to 24.9 cases/100000 persons/year. The proportion of clinical infections increased from 25 to 32% in the 5-year periods, respectively, (p < 0.05). The median age decreased from 61 years in 2007 to 30 years in 2016. HA-MRSA accounted for 68% of all cases, of which 32% associated with 26 healthcare outbreaks. The proportion of CA-MRSA cases increased from 13% in 2007 to 43% in 2016. Of CA-MRSA cases, 43% were among family clusters, 32% in immigrants and 4% were LA-MRSA. The Gini-Simpson diversity index for spa types increased from 0.86 to 0.95 from the first to the second 5-year period. The proportion of a predominant strain t172 decreased from 43% in 2009 to 7% in 2016. The rise in the proportion of CA-MRSA, the switch to younger age groups, the complexity of possible transmission routes and the growing spa-type diversity characterize our current MRSA landscape. This creates challenges for targeted infection control measures, demanding further studies.

Longitudinal, strain-specific Staphylococcus aureus introduction and transmission events in households of children with community-associated meticillin-resistant S aureus skin and soft tissue infection: a prospective cohort study

BACKGROUND

Devising effective, targeted approaches to prevent recurrent meticillin-resistant Staphylococcus aureus (MRSA) skin and soft tissue infection requires an understanding of factors driving MRSA acquisition. We comprehensively defined household longitudinal, strain-level S aureus transmission dynamics in households of children with community-associated MRSA skin and soft tissue infection.

METHODS

From 2012-15, otherwise healthy paediatric patients with culture-confirmed, community-onset MRSA infections were recruited for the Household Observation of MRSA in the Environment (HOME) prospective cohort study from hospitals and community practices in metropolitan St Louis (MO, USA). Children with health-care-related risk factors were excluded, as determined by evidence of recent hospital admission, an invasive medical device, or residence in a long-term care facility. Household contacts (individuals sleeping in the home ≥four nights per week) and indoor dogs and cats were also enrolled. A baseline visit took place at the index patient's primary home, followed by four quarterly visits over 12 months. At each visit, interviews were done and serial cultures were collected, to detect S aureus from three anatomic sites of household members, two anatomic sites on dogs and cats, and 21 environmental surfaces. Molecular typing was done by repetitive-sequence PCR to define distinct S aureus strains within each household. Longitudinal, multivariable generalised mixed-effects logistic regression models identified factors associated with S aureus acquisition.

FINDINGS

Across household members, pets, and environmental surfaces, 1267 strain acquisition events were observed. Acquisitions were driven equally by 510 introductions of novel strains into households and 602 transmissions within households, each associated with distinct factors. Frequent handwashing decreased the likelihood of novel strain introduction into the household (odds ratio [OR] 0·86, credible interval [CrI] 0·74-1·01). Transmission recipients were less likely to own their homes (OR 0·77, CrI 0·63-0·94) and were more likely to share bedrooms with strain-colonised individuals (OR 1·33, CrI 1·12-1·58), live in homes with higher environmental S aureus contamination burden (OR 3·97, CrI 1·96-8·20), and report interval skin and soft tissue infection (OR 1·32, CrI 1·07-1·64). Transmission sources were more likely to share bath towels (OR 1·25, CrI 1·01-1·57). Pets were often transmission recipients, but rarely the sole transmission source.

INTERPRETATION

The household environment plays a key role in transmission, a factor associated with skin and soft tissue infection. Future interventions should inclusively target household members and the environment, focusing on straightforward changes in hand hygiene and household sharing behaviours.

FUNDING

National Institutes of Health, Agency for Healthcare Research and Quality, Children's Discovery Institute, Burroughs Wellcome Foundation, Defense Advanced Research Projects Agency.

Prevention Strategies for Recurrent Community-Associated Staphylococcus aureus Skin and Soft Tissue Infections

PURPOSE OF REVIEW

Staphylococcus aureus skin and soft tissue infections (SSTI) are a major source of morbidity. More than half of patients experiencing SSTI will have at least one recurrent infection. These infections frequently cluster in households. Given the burden these infections pose to patients and healthcare, prevention strategies are of major clinical importance and represent an active area of research. Bacterial colonization is frequently an early and critical step in the pathogenesis of infection. As such, strategies to prevent reinfection have aimed to decrease staphylococcal colonization of the skin and mucus membranes, a process referred to as decolonization.

RECENT FINDINGS

Treatment of acute SSTI with incision and drainage and systemic antibiotics is the mainstay of therapy for healing of the acute infection. Systemic antibiotics also provide benefit through reduced incidence of recurrent SSTI. Education for patients and families regarding optimization of personal and household hygiene measures, and avoidance of sharing personal hygiene items, is an essential component in prevention efforts. For patients experiencing recurrent SSTI, or in households in which multiple members have experienced SSTI, decolonization should be recommended for all household members. A recommended decolonization regimen includes application of intranasal mupirocin and antiseptic body washes with chlorhexidine or dilute bleach water baths. For patients who continue to experience recurrent SSTI, periodic decolonization should be considered. Personal decolonization with topical antimicrobials and antiseptics reduces the incidence of recurrent S. aureus SSTI. Future avenues for investigation include strategies for household environmental decontamination as well as manipulation of the host microbiota.