Molecular and Clinical Epidemiology of SARS-CoV-2 Infection among Vaccinated and Unvaccinated Individuals in a Large Healthcare Organization from New Jersey

New Jersey was among the first states impacted by the COVID-19 pandemic, with one of the highest overall death rates in the nation. Nevertheless, relatively few reports have been published focusing specifically on New Jersey. Here we report on molecular, clinical, and epidemiologic observations, from the largest healthcare network in the state, in a cohort of vaccinated and unvaccinated individuals with laboratory-confirmed SARS-CoV-2 infection. We conducted molecular surveillance of SARS-CoV-2-positive nasopharyngeal swabs collected in nine hospitals from December 2020 through June 2022, using both whole genome sequencing (WGS) and a real-time RT-PCR screening assay targeting spike protein mutations found in variants of concern (VOCs) within our region. De-identified clinical data were obtained retrospectively, including demographics, COVID-19 vaccination status, ICU admission, ventilator support, mortality, and medical history. Statistical analyses were performed to identify associations between SARS-CoV-2 variants, vaccination status, clinical outcomes, and medical risk factors. A total of 5007 SARS-CoV-2-positive nasopharyngeal swabs were successfully screened and/or sequenced. Variant screening identified three predominant VOCs, including Alpha (n = 714), Delta (n = 1877), and Omicron (n = 1802). Omicron isolates were further sub-typed as BA.1 (n = 899), BA.2 (n = 853), or BA.4/BA.5 (n = 50); the remaining 614 isolates were classified as "Other". Approximately 31.5% (1577/5007) of the samples were associated with vaccine breakthrough infections, which increased in frequency following the emergence of Delta and Omicron. Severe clinical outcomes included ICU admission (336/5007 = 6.7%), ventilator support (236/5007 = 4.7%), and mortality (430/5007 = 8.6%), with increasing age being the most significant contributor to each (p < 0.001). Unvaccinated individuals accounted for 79.7% (268/336) of ICU admissions, 78.3% (185/236) of ventilator cases, and 74.4% (320/430) of deaths. Highly significant (p < 0.001) increases in mortality were observed in individuals with cardiovascular disease, hypertension, cancer, diabetes, and hyperlipidemia, but not with obesity, thyroid disease, or respiratory disease. Significant differences (p < 0.001) in clinical outcomes were also noted between SARS-CoV-2 variants, including Delta, Omicron BA.1, and Omicron BA.2. Vaccination was associated with significantly improved clinical outcomes in our study, despite an increase in breakthrough infections associated with waning immunity, greater antigenic variability, or both. Underlying comorbidities contributed significantly to mortality in both vaccinated and unvaccinated individuals, with increasing risk based on the total number of comorbidities. Real-time RT-PCR-based screening facilitated timely identification of predominant variants using a minimal number of spike protein mutations, with faster turnaround time and reduced cost compared to WGS. Continued evolution of SARS-CoV-2 variants will likely require ongoing surveillance for new VOCs, with real-time assessment of clinical impact.

Enantiomeric glycosylated cationic block co-beta-peptides eradicate Staphylococcus aureus biofilms and antibiotic-tolerant persisters

The treatment of bacterial infections is hindered by the presence of biofilms and metabolically inactive persisters. Here, we report the synthesis of an enantiomeric block co-beta-peptide, poly(amido-D-glucose)-block-poly(beta-L-lysine), with high yield and purity by one-shot one-pot anionic-ring opening (co)polymerization. The co-beta-peptide is bactericidal against methicillin-resistant Staphylococcus aureus (MRSA), including replicating, biofilm and persister bacterial cells, and also disperses biofilm biomass. It is active towards community-acquired and hospital-associated MRSA strains which are resistant to multiple drugs including vancomycin and daptomycin. Its antibacterial activity is superior to that of vancomycin in MRSA mouse and human ex vivo skin infection models, with no acute in vivo toxicity in repeated dosing in mice at above therapeutic levels. The copolymer displays bacteria-activated surfactant-like properties, resulting from contact with the bacterial envelope. Our results indicate that this class of non-toxic molecule, effective against different bacterial sub-populations, has promising potential for the treatment of S. aureus infections.

The authors report the synthesis of an enantiomeric block co-beta-peptide that kills methicillin-resistant Staphylococcus aureus, including biofilm and persister bacterial cells, and disperses biofilms. The copolymer displays antibacterial activity in human ex vivo and mouse in vivo infection models without toxicity.

Genetic Diversity of Carbapenem-Resistant Enterobacteriaceae (CRE) Clinical Isolates From a Tertiary Hospital in Eastern China

The prevalence of carbapenem-resistant Enterobacteriaceae (CRE) is increasing globally, with different molecular mechanisms described. Here we studied the molecular mechanisms of carbapenem resistance, including clonal and plasmid dissemination, of 67 CRE isolates collected between 2012 and 2016 from a tertiary hospital in Eastern China, an CRE endemic region. Species identification and susceptibility testing were performed using the BD Phoenix Automated Microbiology System. Isolates were characterized by PCR (for carbapenemases, ESBLs, AmpC and porin genes), multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and conjugation transfer experiments. Selected bla_KPC-2 -harboring plasmids were subjected to next-generation sequencing using the Illumina Miseq platform. Among the 67 CRE isolates, 42 Klebsiella pneumoniae, 10 Serratia marcescens, 6 Enterobacter cloacae, 2 Raoultella ornithinolytica, 2 K. oxytoca, 1 K. aerogenes, and 4 Escherichia coli isolates were identified. Six different carbapenemases were detected, including bla_KPC-2 (n = 45), bla_KPC-3 (n = 1), bla_NDM-1 (n = 6), bla_NDM-5 (n = 1), bla_IMP-4 (n = 2), and bla_VIM-1 (n = 2); bla_OXA-48-like genes were not detected. One E. cloacae strain possessed both bla_NDM-1 and bla_KPC-3, while two E. cloacae isolates harbored bla_NDM-1 and bla_VIM-1. ESBLs (CTX-M, SHV, and TEM) and/or AmpC (CMY, DHA, and ACT/MIR) genes were also identified in 59 isolates, including 13 strains that lacked carbapenemases. Several insertions or stop codon mutations were found within porin genes of K. pneumoniae, E. coli and S. marcescens isolates, both with and without carbapenemases. The 42 K. pneumoniae isolates belonged to 12 different sequence types (ST), with ST11 being the most common, while the 6 E. cloacae isolates comprised 4 different STs. The 10 S. marcescens all shared the same PFGE pulsotype, suggestive of clonal spread. Complete plasmid sequencing and PCR screening revealed both intra-strain and inter-species spread of a common bla_KPC-2-harboring plasmid in our hospital. Taken together, our study revealed extensive genetic diversity among CRE isolates form a single Chinese hospital. CRE isolates circulating in the hospital differ significantly in their species, STs, porin genes, carbapenemase genes, and their plasmid content, highlighting the complex dissemination of CRE in this endemic region.

MRSA clonal complex 22 strains harboring toxic shock syndrome toxin (TSST-1) are endemic in the primary hospital in Gaza, Palestine

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen in both community and healthcare-related settings worldwide. Current knowledge regarding the epidemiology of S. aureus and MRSA in Gaza is based on a single community-based carriage study. Here we describe a cross-sectional analysis of 215 clinical isolates collected from Al-Shifa Hospital in Gaza during 2008 and 2012.

Methods

All isolates were characterized by spa typing, SCCmec typing, and detection of genes encoding Panton-Valentine leukocidin (PVL) and toxic shock syndrome toxin (TSST-1). Representative genotypes were also subjected to multilocus sequence typing (MLST). Antibiotic susceptibility testing was performed using VITEK2 and MicroScan.

Results

MRSA represented 56.3% of all S. aureus strains, and increased in frequency from 2008 (54.8%) to 2012 (58.4%). Aside from beta-lactams, resistance was observed to tetracycline, erythromycin, clindamycin, gentamicin, and fluoroquinolones. Molecular typing identified 35 spa types representing 17 MLST clonal complexes (CC), with spa 998 (Ridom t223, CC22) and spa 70 (Ridom t044, CC80) being the most prevalent. SCCmec types I, III, IV, V and VI were identified among MRSA isolates, while type II was not detected. PVL genes (lukF/S-PV) were detected in 40.0% of all isolates, while the TSST-1 gene (tst) was detected in 27.4% of all isolates, with surprisingly high frequency within CC22 (70.4%). Both PVL and TSST-1 genes were found in several isolates from 2012.

Conclusions

Molecular typing of clinical isolates from Gaza hospitals revealed unusually high prevalence of TSST-1 genes among CC22 MRSA, which is noteworthy given a recent community study describing widespread carriage of a CC22 MRSA clone known as the ‘Gaza strain’. While the latter did not address TSST-1, tst-positive spa 998 (Ridom t223) has been detected in several neighboring countries, and described as endemic in an Italian NICU, suggesting international spread of a ‘Middle Eastern variant’ of pandemic CC22 strain EMRSA-15.

Methicillin-resistant Staphylococcus aureus sequence type 239-III, Ohio, USA, 2007-2009

Identification of virulent strains emphasizes the need for molecular surveillance.

A comparison of methicillin-resistant and methicillin-susceptible Staphylococcus aureus reveals no clinical and epidemiological but molecular differences

Most studies on Staphylococcus aureus have focused on the molecular epidemiology of methicillin-resistant S. aureus (MRSA) infections. In contrast, little information is available regarding the molecular epidemiology of currently circulating methicillin-susceptible S. aureus (MSSA) isolates in hospital settings, an epoch when the epidemiology of S. aureus has undergone significant changes. We conducted a cross-sectional study to compare the clinical, epidemiological, and genetic characteristics of MSSA and MRSA isolates at 3 tertiary-care hospitals in Medellín, Colombia, from February 2008 to June 2010. The infections were classified according to the Centers for Disease Control and Prevention (CDC) definitions. Genotypic analysis included spa typing, multilocus sequence typing (MLST) and staphylococcal cassette chromosome (mec) (SCCmec) typing. A total of 810 patients was enrolled. One hundred infections (12.3%) were classified as community-associated (31 CA-MSSA, 69 CA-MRSA), 379 (46.8%) as healthcare-associated community-onset (136 HACO-MSSA, 243 HACO-MRSA), and 331 (40.9%) as healthcare-associated hospital-onset (104 HAHO-MSSA, 227 HAHO-MRSA). Genotype analyses showed a higher diversity and a more varied spa type repertoire in MSSA than in MRSA strains. Most of the clinical-epidemiological characteristics and risk factors evaluated did not allow for discriminating MRSA- from MSSA-infected patients. The lack of equivalence among the genetic backgrounds of the major MSSA and MRSA clones would suggest that the MRSA clones are imported instead of arising from successful MSSA clones. This study emphasizes the importance of local surveillance to create public awareness on the changing S. aureus epidemiology.

Clinical and molecular epidemiology of methicillin-resistant Staphylococcus aureus among patients in an ambulatory hemodialysis center

OBJECTIVE

To describe the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) carriage and transmission in an ambulatory hemodialysis population.

DESIGN

Prospective cohort study.

SETTING

Outpatient hemodialysis facility affiliated with a large academic medical center.

PARTICIPANTS

Of the 170 facility patients, 103 (61%) participated in the study.

METHODS

Swab specimens of the nares, axillae, and vascular access site were collected from participants weekly for 3 weeks and then monthly for 5 months. Demographic and clinical data were collected monthly for 12 months. Molecular analysis of MRSA isolates was performed.

RESULTS

The baseline MRSA carriage prevalence was 12%. Factors associated with MRSA carriage included a history of MRSA; failed renal transplantation; hospital admission within 6 months; and receipt of a first-generation cephalosporin, cefepime, or vancomycin. Six subjects acquired MRSA after enrollment (incidence, 1.2 per 100 patient-months at-risk; overall prevalence, 18%). Molecular analysis suggested that transmission occurred within the facility. The incidence of MRSA infection among carriers was 1.76 per 100 patient-months. Community-associated strains (ie, USA300) were isolated from 28% of carriers and at least 25% of infections.

CONCLUSIONS

The prevalence of MRSA carriage and the incidence of infection among carriers were high among ambulatory hemodialysis patients, and community-associated MRSA was responsible for a large portion of the MRSA burden. A relatively high rate of MRSA acquisition was observed, with indirect evidence of intrafacility transmission. Additional studies are needed to confirm these findings and to identify effective and feasible methods to prevent MRSA transmission and infection among hemodialysis patients.

Molecular characterization and antibiotic susceptibility of Staphylococcus aureus from a multidisciplinary hospital in Romania

From 2004 to 2005, 60%-72% of invasive Staphylococcus aureus isolates from Romanian hospitals were resistant to methicillin (methicillin-resistant S. aureus [MRSA]), the highest frequency for any European nation. Few reports, however, have addressed the molecular characteristics of S. aureus in Romania. In this study, we utilized spa typing, multilocus sequence typing, staphylococcal cassette chromosome mec (SCCmec) typing, dru typing, pulsed-field gel electrophoresis, and detection of virulence factors to characterize 146 S. aureus strains isolated from 2004 to 2005 at the Clinic County Hospital in Braşov. Antibiotic susceptibility patterns for all MRSA isolates and patient demographic data were also obtained. Fifty-six strains (38.4%) were determined to be MRSA by susceptibility testing and SCCmec typing. All MRSA strains were resistant to beta-lactams and tetracycline, but susceptible to nitrofurans, vancomycin, and clindamycin, with inducible clindamycin resistance in 23/28 clindamycin-sensitive/erythromycin-resistant isolates. Molecular typing identified 15 clonal backgrounds (CC 1, 5, 8, 8/239, 9, 15, 20, 22, 25, 30, 45, 80, 97, 101, and 121), only 4 of which were associated with MRSA (CC 1, 8/239, 30, and 80). Spa types 35 (t127, CC 1) and 351 (t030, CC 8/239) accounted for 27.4% and 21.9% of all S. aureus strains, respectively, and 19.6% and 57.1% of all MRSA strains. Both hospital-associated (SCCmec type III) and community-associated (SCCmec type IV) elements were identified within MRSA strains, whereas Panton-Valentine leukocidin was detected in 10 MRSA and 12 methicillin-sensitive S. aureus strains. These results demonstrate the presence of various endemic S. aureus clones within the Clinic County Hospital in Braşov, suggestive of ongoing nosocomial and community transmission.

Prevalence and characteristics of Staphylococcus aureus colonization among healthcare professionals in an urban teaching hospital

OBJECTIVE

To determine the prevalence of asymptomatic carriage of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) among healthcare professionals (HCPs) who experience varying degrees of exposure to ambulatory patients and to genetically characterize isolates.

METHODS

This single-center, cross-sectional study enrolled 256 staff from the intensive care units, emergency department, and prehospital services of an urban tertiary care university hospital in 2008. Occupational histories and nasal samples for S. aureus cultures were obtained. S. aureus isolates were genetically characterized with the use of spa typing and screened for mecA. MRSA isolates underwent further characterization.

RESULTS

S. aureus was isolated from 112 of 256 (43.8%) HCPs, including 30 of 52 (57.7%) paramedics, 51 of 124 (41.1%) nurses, 11 of 28 (39.3%) clerical workers, and 20 of 52 (38.5%) physicians. MRSA was isolated from 17 (6.6%) HCPs, including 1 (1.9%) paramedic, 13 (10.5%) nurses, 1 (3.6%) clerical worker, and 2 (3.8%) physicians. Among S. aureus isolates, 15.2% were MRSA. MRSA prevalence was 9.6% (12/125) in emergency department workers, 5.1% (4/79) in intensive care unit workers, and 1.9% (1/52) in emergency medical services workers. Compared with paramedics, who had the lowest prevalence of methicillin resistance among S. aureus isolates (1 of 30 [3.3%] isolates), nurses, who had the highest prevalence (13 of 51 [25.4%] isolates), had an odds ratio of 9.92 (95% confidence interval, 1.32-435.86; P = .02) for methicillin resistance. Analysis of 15 MRSA isolates revealed 7 USA100 strains, 6 USA300 strains, 1 USA800 strain, and 1 EMRSA-15 strain. All USA300 strains were isolated from emergency department personnel.

CONCLUSIONS

The observed prevalence of S. aureus and MRSA colonization among HCPs exceeds previously reported prevalences in the general population. The proportion of community-associated MRSA among all MRSA in this colonized HCP cohort reflects the distribution of the USA300 community-associated strain observed increasingly among US hospitalized patients.