Changing molecular epidemiology and high rates of mupirocin resistance among meticillin-resistant Staphylococcus aureus in Singaporean hospitals

Emergence and clonal expansion of a qacA-harbouring sequence type 45 lineage of methicillin-resistant Staphylococcus aureus

The past decade has seen an increase in the prevalence of sequence type (ST) 45 methicillin-resistant Staphylococcus aureus (MRSA), yet the underlying drivers for its emergence and spread remain unclear. To better understand the worldwide dissemination of ST45 S. aureus, we performed phylogenetic analyses of Australian isolates, supplemented with a global population of ST45 S. aureus genomes. Our analyses revealed a distinct lineage of multidrug-resistant ST45 MRSA harbouring qacA, predominantly found in Australia and Singapore. Bayesian inference predicted that the acquisition of qacA occurred in the late 1990s. qacA was integrated into a structurally variable region of the chromosome containing Tn552 (carrying blaZ) and Tn4001 (carrying aac(6')-aph(2")) transposable elements. Using mutagenesis and in vitro assays, we provide phenotypic evidence that qacA confers tolerance to chlorhexidine. These findings collectively suggest both antimicrobial resistance and the carriage of qacA may play a role in the successful establishment of ST45 MRSA.

Diversity and Dissemination of Methicillin-Resistant Staphylococcus aureus (MRSA) Genotypes in Southeast Asia

Methicillin-resistant Staphylococcus aureus (MRSA) is a successful pathogen that has achieved global dissemination, with high prevalence rates in Southeast Asia. A huge diversity of clones has been reported in this region, with MRSA ST239 being the most successful lineage. Nonetheless, description of MRSA genotypes circulating in the Southeast Asia region has, until now, remained poorly compiled. In this review, we aim to provide a better understanding of the molecular epidemiology and distribution of MRSA clones in 11 Southeast Asian countries: Singapore, Malaysia, Thailand, Vietnam, Cambodia, Lao People's Democratic Republic (PDR), Myanmar, Philippines, Indonesia, Brunei Darussalam, and Timor-Leste. Notably, while archaic multidrug-resistant hospital-associated (HA) MRSAs, such as the ST239-III and ST241-III, were prominent in the region during earlier observations, these were then largely replaced by the more antibiotic-susceptible community-acquired (CA) MRSAs, such as ST22-IV and PVL-positive ST30-IV, in recent years after the turn of the century. Nonetheless, reports of livestock-associated (LA) MRSAs remain few in the region.

Designing a leucine-rich antibacterial nonapeptide with potent activity against mupirocin-resistant MRSA via a structure-activity relationship study

Staphylococcus aureus is the main aetiological agent responsible for the majority of human skin infections. Of particular concern is the methicillin-resistant variety, commonly known as MRSA. The extensive use of the first-line topical antibiotic of choice, mupirocin, has inevitably resulted in the emergence of resistant strains, signalling an urgent need for the development of new antibacterials with new mechanisms of action. In this work, we describe how we designed a novel cationic nonapeptide, containing only leucine and two lysine residues, with potent anti-MRSA activity and a rapid bactericidal mode of action. Coupled to a favourable safety profile towards human skin fibroblasts, we believe nonapeptide 11 has high potential for further development as a mupirocin replacement candidate to treat skin infections caused by MRSA.

Chlorhexidine-impregnated sponge dressing for prevention of catheter exit-site infection in peritoneal dialysis patients: a pilot study

PURPOSE

The study aimed to examine effect of chlorhexidine dressing in the prevention of peritoneal dialysis (PD)-related infection in PD patients.

METHODS

This single-center pilot study recruited 50 incident PD patients to use weekly chlorhexidine dressing. The primary outcome was exit-site/tunnel infection rate. Secondary outcomes were peritonitis rate, time to first PD-related infection, infection-related hospitalization, technique and patient survival, adverse events, and chlorhexidine dressing acceptability. These clinical outcomes were compared with those of a historical cohort (2016-2017) using daily gentamicin cream.

RESULTS

A total of 50 patients were recruited to use chlorhexidine and followed up for one year. The exit-site/tunnel infection rate was 0.09 (95% confidence interval [CI] 0.02-0.22) and peritonitis rate was 0.07 (95% CI 0.01-0.19) episodes per patient-year with chlorhexidine dressing. The 1-year infection-free survival rates for exit-site/tunnel infection and peritonitis were 92% and 94%, respectively. The 1-year technique and patient survival rates were 86% and 96%, respectively. Overall, 12% of participants developed localized contact dermatitis with chlorhexidine. Most participants (73%) reported that chlorhexidine dressings were very acceptable. Compared to a historical cohort using gentamicin cream (n = 238), the chlorhexidine group had similar exit-site/tunnel infection rates (incidence rate ratio [IRR] 0.65, 95% CI 0.22-1.92) but had lower peritonitis rates (IRR 0.24, 95% CI 0.07-0.77), and lower PD infection-related hospitalization rates (IRR 0.21, 95% CI 0.06-0.69) after adjusting for age, sex, race, primary kidney disease, and diabetes mellitus.

CONCLUSION

Weekly chlorhexidine dressing was associated with acceptable PD-related infection outcomes and was well-accepted by patients, although had a 12% rate of delayed localized contact dermatitis.

TRIAL REGISTRATION NUMBER AND DATE

The study was registered under www.clinicaltrials.gov with the reference number of NCT03406520 on 23 January 2018.

Comparative epidemiology and factors associated with major healthcare-associated methicillin-resistant Staphylococcus aureus clones among interconnected acute-, intermediate- and long-term healthcare facilities in Singapore

OBJECTIVES

Methicillin-resistant Staphylococcus aureus (MRSA) has spread across countries and healthcare settings, with different clones occupying different ecological niches. It is crucial to understand the comparative epidemiology of MRSA clones between healthcare settings and independent factors associated with colonization of specific clones.

METHODS

We conducted annual cross-sectional surveillance studies in a network comprising an acute-care hospital and six closely-affiliated intermediate- and long-term care facilities in Singapore between June and July, 2014-2016; 5394 patients contributed 16 045 nasal, axillary and groin samples for culture and MRSA isolates for whole-genome sequencing. Multivariable multilevel multinomial regression models were constructed to assess independent factors associated with MRSA colonization.

RESULTS

MRSA clonal complex (CC) 22 was more prevalent in the acute-care hospital (n = 256/493; 51.9%) and intermediate-care facilities (n = 348/634; 54.9%) than in long-term care (n = 88/351; 25.1%) facilities, with clones other than CC22 and CC45 being more prevalent in long-term care facilities (n = 144/351; 41.0%) (p < 0.001). Groin colonization with CC45 was six times that of nasal colonization (aOR 6.21, 95%CI 4.26-9.01). Prior MRSA carriage was associated with increased odds of current MRSA colonization in all settings, with a stronger association with CC22 (aOR 6.45, 95%CI 3.85-10.87) than CC45 (aOR 4.15, 95%CI 2.26-7.58).

CONCLUSIONS

Colonization by MRSA clones differed between anatomical sites and across healthcare settings. With CC22 having a predilection for the nares and CC45 the groin, MRSA screening should include both sites. Prior MRSA carriage is a risk factor for colonization with predominant MRSA clones in the acute-care hospital and intermediate- and long-term care facilities. Contact precautions for prior MRSA carriers on admission to any healthcare facility could prevent intra- and inter-institutional MRSA transmission.

Impact of formulary interventions on the minimum inhibitory concentration of methicillin-resistant Staphylococcus aureus to mupirocin, chlorhexidine, and octenidine in a Singapore tertiary institution

Methicillin-resistant Staphylococcus aureus (MRSA) decolonization is an effective measure to prevent clinical infection but resistance is a concern. We aim to evaluate the impact of mupirocin (MUP) ointment formulary removal, plateauing use of chlorhexidine gluconate (CHG), and hospital-wide introduction of octenidine (OCT)-based products on the minimum inhibitory concentration (MIC) of MRSA to MUP, CHG, and OCT in our hospital. A prevalence study was conducted at three time points (TP) on consecutive MRSA screening isolates to evaluate for their MICs to MUP, CHG, and OCT using broth microdilution sensititre plates and detection of the ileS-2 gene encoding high-level MUP resistance in 2013 (pre-intervention TP1; n = 160), 2016 (early post-intervention TP2; n = 99) and 2017 (late post-intervention TP3; n = 76). Statistical analyses were performed using Chi square test with reference from TP1. There was a significant improvement in MUP susceptibility (MIC < 4 mcg/ml) from 71.9% (TP1) to 86.9% (TP2; p = 0.006) to 88.2% (TP3; p = 0.007). The prevalence of MUP high-level resistance (MIC > 256 mcg/ml) reduced from 25.0% (TP1) to 12.1% (TP2; p = 0.014) to 5.3% (TP3; p = 0.001). Likewise, the prevalence of isolates harboring the ileS-2 gene decreased from 28.1% (TP1) to 18.2% (TP2; p = 0.072) to 9.2% (TP3; p = 0.002). OCT MIC range remains stable at 0.5 to 1 mcg/ml across all three TPs. The proportion of isolates with reduced CHG susceptibility (MIC ≥ 4 mcg/ml) increased over the three TPs from 23.1 to 27.2% (p = 0.45) to 42.1% (p = 0.003). Active formulary regulations have an impact on the resistance profile of MRSA and can be used as a strategy to preserve the MRSA decolonization armamentarium.

Molecular epidemiology of antimicrobial resistant microorganisms in the 21th century: a review of the literature

Healthcare-associated infections (HAIs) are the most frequent and severe complication acquired in healthcare settings with high impact in terms of morbidity, mortality and costs. Many bacteria could be implicated in these infections, but, expecially multidrug resistance bacteria could play an important role. Many microbial typing technologies have been developed until to the the bacterial whole-genome sequencing and the choice of a molecular typing method therefore will depend on the skill level and resources of the laboratory and the aim and scale of the investigation. In several studies the molecular investigation of pathogens involved in HAIs was performed with many microorganisms identified as causative agents such as Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Clostridium difficile, Acinetobacter spp., Enterobacter spp., Enterococcus spp., Staphylococcus aureus and several more minor species. Here, we will describe the most and least frequently reported clonal complex, sequence types and ribotypes with their worldwide geographic distribution for the most important species involved in HAIs.

Chlorhexidine and octenidine use, carriage of qac genes, and reduced antiseptic susceptibility in methicillin-resistant Staphylococcus aureus isolates from a healthcare network

OBJECTIVES

With the widespread use of antiseptics in healthcare facilities for the prevention of methicillin-resistant Staphylococcus aureus (MRSA) transmission, there are concerns for antiseptic tolerance and resistance. We sought to understand the use of chlorhexidine and octenidine, carriage of qac genes, and reduced antiseptic susceptibilities.

METHODS

A serial cross-sectional study was conducted in an acute care hospital and three extended-care facilities of a healthcare network in June-July, 2014-2016. Two of the extended-care facilities were exposed to intranasal octenidine and universal daily chlorhexidine/octenidine bathing. The minimum inhibitory concentration (MIC) levels and qac genes were determined by broth microdilution tests and whole genome sequencing respectively. Multivariable logistic regression was used to assess for the independent associations between antiseptic exposures, qac genes, and reduced antiseptic susceptibilities.

RESULTS

A total of 878 MRSA isolates were obtained. There were associations between qacA/B carriage and chlorhexidine (adjusted odds ratio (aOR) 7.80; 95% confidence interval (CI) 3.25-18.71) and octenidine (aOR 11.79; 95% CI 5.14-27.04) exposures. Chlorhexidine exposure was associated with reduced chlorhexidine susceptibility (MIC ≥4 mg/L) (aOR 3.15; 95% CI 1.14-8.74). Carriage of qacA/B (aOR 10.65; 95% CI 4.14-27.40) or qacC (aOR 2.55; 95% CI 1.22-5.32) had an association with reduced chlorhexidine susceptibility; while MRSA sequence type modified the association. However, we found no direct association between (i) antiseptics use and qacC carriage, (ii) octenidine exposure and reduced susceptibility, and (iii) reduced octenidine susceptibility and qacA/B or qacC carriage.

CONCLUSIONS

Antiseptic exposures were associated with carriage of qac genes. Chlorhexidine exposure was associated with reduced chlorhexidine susceptibility, requiring continued surveillance for the emergence of resistance.

Significant Enrichment and Diversity of the Staphylococcal Arginine Catabolic Mobile Element ACME in Staphylococcus epidermidis Isolates From Subgingival Peri-implantitis Sites and Periodontal Pockets

Staphylococcus aureus and Staphylococcus epidermidis are frequent commensals of the nares and skin and are considered transient oral residents. Reports on their prevalence in the oral cavity, periodontal pockets and subgingivally around infected oral implants are conflicting, largely due to methodological limitations. The prevalence of these species in the oral cavities, periodontal pockets and subgingival sites of orally healthy individuals with/without implants and in patients with periodontal disease or infected implants (peri-implantitis) was investigated using selective chromogenic agar and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Staphylococcus epidermidis was predominant in all participant groups investigated. Its prevalence was significantly higher (P = 0.0189) in periodontal pockets (30%) than subgingival sites of healthy individuals (7.8%), and in subgingival peri-implantitis sites (51.7%) versus subgingival sites around non-infected implants (16.1%) (P = 0.0057). In contrast, S. aureus was recovered from subgingival sites of 0-12.9% of the participant groups, but not from periodontal pockets. The arginine catabolic mobile element (ACME), thought to enhance colonization and survival of S. aureus, was detected in 100/179 S. epidermidis and 0/83 S. aureus isolates screened using multiplex PCR and DNA microarray profiling. Five distinct ACME types, including the recently described types IV and V (I; 14, II; 60, III; 10, IV; 15, V; 1) were identified. ACME-positive S. epidermidis were significantly (P = 0.0369) more prevalent in subgingival peri-implantitis sites (37.9%) than subgingival sites around non-infected implants (12.9%) and also in periodontal pockets (25%) compared to subgingival sites of healthy individuals (4.7%) (P = 0.0167). To investigate the genetic diversity of ACME, 35 isolates, representative of patient groups, sample sites and ACME types underwent whole genome sequencing from which multilocus sequence types (STs) were identified. Sequencing data permitted ACME types II and IV to be subdivided into subtypes IIa-c and IVa-b, respectively, based on distinct flanking direct repeat sequences. Distinct ACME types were commonly associated with specific STs, rather than health/disease states or recovery sites, suggesting that ACME types/subtypes originated amongst specific S. epidermidis lineages. Ninety of the ACME-positive isolates encoded the ACME-arc operon, which likely contributes to oral S. epidermidis survival in the nutrient poor, semi-anaerobic, acidic and inflammatory conditions present in periodontal disease and peri-implantitis.

Preliminary investigations into developing all-D Omiganan for treating Mupirocin-resistant MRSA skin infections

Staphylococcus aureus is the primary pathogen responsible for the majority of human skin infections, and meticillin-resistant S. aureus (MRSA) currently presents a major clinical concern. The overuse of Mupirocin, the first-line topical antibacterial drug over 30 years, has led to the emergence of Mupirocin-resistant MRSA, creating a clinical concern. The antimicrobial peptide Omiganan was touted to be a promising antibacterial drug candidate due to its rapid membrane-disrupting bactericidal mode of action, entering clinical trials in 2005 as a topical gel to prevent catheter site infections. However, drug development ceased in 2009 due to a lack of efficacy. We postulate this to be due to proteolytic degradation caused by endogenous human skin proteases. Herein, we tested our hypothesis using Omiganan and its all-D enantiomer in a human skin protease stability assay, followed by anti-MRSA activity assay against of a panel of clinical MRSA isolates, a bactericidal/static determination and a time-kill assay to gauge all-D Omiganan's potential for further topical antibacterial drug development.

Emerging multidrug-resistant Bengal Bay clone ST772-MRSA-V in Norway: molecular epidemiology 2004-2014

A multidrug-resistant, methicillin-resistant Staphylococcus aureus (MRSA) clone, PVL-positive ST772-MRSA-V, named the Bengal Bay clone, is emerging worldwide. In Norway, where MRSA prevalence is low, a sudden increase in ST772-MRSA-V initiated a nationwide molecular epidemiological study. Clinical data were obtained from the Norwegian Surveillance System for Communicable Diseases (MSIS). S. aureus isolates were characterised by antibiotic susceptibility profiles and comprehensive genotyping (spa typing, MLVA, DNA microarray). ST772-MRSA was detected in 145 individuals during 2004-2014, with 60% of cases occurring in 2013-2014. Median age was 31 years and male/female ratio 1.16. The majority had a family background from the Indian subcontinent (70%). MRSA acquisition was mainly reported as unknown (39%) or abroad (42%), the latter associated with a home-country visit (59%), tourism (16%), and immigration (13%). Clinical infection was present in 75%, predominantly by SSTI (83%), 18% were admitted to hospital and 42% were linked to small-scale outbreaks (n = 25). All isolates were multidrug-resistant. Most isolates were resistant to erythromycin, gentamicin and norfloxacin. Genotyping revealed a conserved clone predominated by spa type t657 (83%), MLVA-type 432 (67%) and the genes lukF/S, sea, sec/sel, egc, scn, cna, ccrAA/ccrC, agrII and cap5. A few untypical ccr gene combinations were detected. Bengal Bay isolates have likely been imported on several occasions and revision of infection control guidelines may prevent further spread.

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.

Comparison of Topical Chlorhexidine and Mupirocin for the Prevention of Exit-Site Infection in Incident Peritoneal Dialysis Patients

♦ OBJECTIVE: Prevention of exit-site infection (ESI) is of paramount importance to peritoneal dialysis (PD) patients. The aim of this study was to evaluate the effectiveness of chlorhexidine in the prevention of ESI in incident PD patients compared with mupirocin. ♦ METHODS: This retrospective, pre-test/post-test observational study included all incident PD patients at Singapore General Hospital from 2012 to 2015. Patients received daily topical exit-site application of either mupirocin (2012 - 2013) or chlorhexidine (2014 - 2015) in addition to routine exit-site cleaning with 10% povidone-iodine. The primary outcome was ESI rate during the 2 time periods. Secondary outcomes were peritonitis rate, times to first ESI and peritonitis, hospitalization rate, and infection-related catheter removal. Event rates were analyzed using Poisson regression, and infection-free survival was estimated using Kaplan-Meier and Cox regression survival analyses. ♦ RESULTS: The study included 162 patients in the mupirocin period (follow-up 141.5 patient-years) and 175 patients in the chlorhexidine period (follow-up 136.9 patient-years). Compared with mupirocin-treated patients, chlorhexidine-treated patients experienced more frequent ESIs (0.22 vs 0.12 episodes/patient-year, p = 0.048), although this was no longer statistically significant following multivariable analysis (incidence rate ratio [IRR] 1.78, 95% confidence interval [CI] 0.98 - 3.26, p = 0.06). No significant differences were observed between the 2 groups with respect to time to first ESI (p = 0.10), peritonitis rate (p = 0.95), time to first peritonitis (p = 0.60), hospitalization rate (p = 0.21) or catheter removal rate (0.03 vs 0.04/patient-year, p = 0.56). ♦ CONCLUSIONS: Topical exit-site application of chlorhexidine cream was associated with a borderline significant, higher rate of ESI in incident PD patients compared with mupirocin cream.

Decolonization and decontamination: what's their role in infection control?

PURPOSE OF REVIEW

Hospital-acquired infections cause up to 19% of infections in paediatric patients contributing to the spread of antimicrobial resistance. This review evaluates the effect of decolonization and decontamination in hospitalized children and neonates as an adjunct to standard infection control measures.

RECENT FINDINGS

Few studies on decolonization and decontamination are available in children. The evidence about the effectiveness of daily chlorhexidine washcloths on bacteraemia in paediatric patients relies on a single randomized controlled trial, in neonates with central venous access in a single retrospective observational study. It is uncertain whether nasal mupirocin reduces methicillin-resistant Staphylococcus aureus carriage and infections in neonates, whereas oral chlorhexidine mouthwashes have not proven effective in children in intensive care settings. Scanty evidence demonstrates a reduction in the rate of ventilation-acquired pneumonia with digestive tract decontamination in paediatric patients and no studies are available in neonates. These strategies have not been extensively tested in resource-poor countries.

SUMMARY

Strong evidence about the efficacy of decolonization and decontamination interventions exists in adult medicine but not in paediatric patients. There is an urgent need to understand how these interventions could be adapted to neonates and resource-poor settings in which the prevalence of hospital-acquired infections is higher.