Genomic Basis of Occurrence of Cryptic Resistance among Oxacillin- and Cefoxitin-Susceptible mecA-Positive Staphylococcus aureus

Potential Impact of Rapid Molecular Microbiologic Diagnosis for Mechanically Ventilated Children in Intensive Care With Suspected Pneumonia

BACKGROUND

Lower respiratory tract infections (LRTIs) remain a leading cause of community-acquired and nosocomial infection in children and a common indication for antimicrobial use and intensive care admission. Determining the causative pathogen for LRTIs is difficult and traditional culture-based methods are labor- and time-intensive. Emerging molecular diagnostic tools may identify pathogens and detect antimicrobial resistance more quickly, to enable earlier targeted antimicrobial therapy.

METHODS

This is a single-center, prospective observational laboratory study evaluating the use of the Biofire FilmArray pneumonia panel (FA-PP) (BioFire Diagnostics, Salt Lake City, UT) for bronchoalveolar lavage specimens from mechanically ventilated children admitted with suspected or presumed pneumonia. We aimed to determine its feasibility and utility for identifying pathogens, antimicrobial resistance and its potential influence on antibiotic prescribing.

RESULTS

We analyzed 50 samples taken from 41 children with a median age of 6 months. Positive agreement between culture and FA-PP was 83% and negative agreement was 76%. Agreement between FA-PP ( mecA/C or MREJ ) and culture was high for methicillin-resistant Staphylococcus aureus . In 3 cases, extended-spectrum beta-lactamase-producing Gram-negative organisms were detected by culture and not FA-PP. Hypothetically, FA-PP results would have affected antimicrobial prescribing in approximately half the cases (24, 48%).

CONCLUSIONS

FA-PP is a useful adjunct to traditional culture methods in mechanically ventilated children with LRTIs and may influence clinical decision-making regarding antibiotic escalation or stewardship.

Characterization of Oxacillin-Resistant and Oxacillin-Susceptible mecA-Positive Staphylococcus pseudintermedius from Skin Lesions and Nasal Cavities of Dogs with Clinical Pyoderma

Understanding the epidemiology of mecA-positive Staphylococcus pseudintermedius strains, including those that are oxacillin-susceptible but potentially inducible to resistance, is crucial for developing effective treatment strategies and mitigating public health risks. This study characterized 87 mecA-positive S. pseudintermedius isolates obtained from skin lesions and nasal orifices of 46 dogs with pyoderma enrolled at a referral hospital in Thailand between 2019 and 2020. All isolates underwent antibiogram profiling, SCCmec typing, and pulsed-field gel electrophoresis (PFGE) for phenotypic and genetic analysis. Among the 87 isolates, 33 isolates (37.9%) recovered from 15 dogs were oxacillin-resistant (OR-MRSP), while 54 isolates (62.1%) from 31 dogs were oxacillin-susceptible (OS-MRSP). All OR-MRSP isolates exhibited multidrug resistance (MDR), and 44% of the OS-MRSP isolates also showed MDR. SCCmec typing revealed type V as predominant among OR-MRSP isolates (69.7%), while many oxacillin-susceptible isolates (70.4%) were non-typeable. The OR-MRSP isolates from the same dog showed consistent antibiogram and SCCmec types, while OS-MRSP isolates displayed both identical and diverse patterns. No dominant pulsotypes were observed among the OR-MRSP or OS-MRSP strains. Genetic diversity was also noted among the isolates within the same dogs and among the others, highlighting the complexity of S. pseudintermedius colonization and infection dynamics in pyoderma-affected dogs.

Molecular characteristics and evaluation of the phenotypic detection of carbapenemases among Enterobacterales and Pseudomonas via whole genome sequencing

Background/purposes

The continuously increasing carbapenem resistance within Enterobacterales and Pseudomonas poses a threat to public health, nevertheless, the molecular characteristics of which in southern China still remain limited. And carbapenemase identification is a key factor in effective early therapy of carbapenem-resistant bacteria infections. We aimed to determine the molecular characteristics of these pathogens and compare commercial combined disc tests (CDTs) with the modified carbapenem inactivation method (mCIM) and EDTA-CIM (eCIM) in detecting and distinguishing carbapenemases using whole genome sequencing (WGS).

Methods

A total of 78 Enterobacterales, 30 Pseudomonas were obtained from two tertiary hospitals in southern China. Susceptibility tests were conducted using an automated VITEK2 compact system with confirmation via the Kirby-Bauer method. The WGS was conducted on all clinical isolates and the molecular characteristics were analyzed by screening the whole genome sequences. CDTs with or without cloxacillin, mCIM, and eCIM, were performed and compared by taking WGS results as the benchmark.

Results

A total of 103 carbapenem non-susceptible and 5 carbapenem susceptible bacteria were determined, with Klebsiella pneumoniae (42.7%), Pseudomonas aeruginosa (23.3%) and Escherichia coli (18.4%) being most prevalent. Carbapenemase genes were detected in 58 (56.3%) of the 103 carbapenem-non-susceptible clinical isolates, including 46 NDM, 6 KPC, 3 IMP, 1 IPM+VIM,1NDM+KPC, and 1 OXA-181. Carbapenemase-producing isolates were detected more frequently in Enterobacterales (76.3%). Among K. pneumoniae, the major sequence types were st307 and st11, while among E. coli and P. aeruginosa, the most prevalent ones were st410 and st242 respectively. For carbapenemase detection in Enterobacterales, the mCIM method achieved 100.00% (95% CI, 92.13-100.00%) sensitivity and 94.44% (70.63-99.71%) specificity (kappa, 0.96); for Pseudomonas, detection sensitivity was 100% (5.46-100.00%), and 100% (84.50-100.00%) specificity (kappa, 0.65). Commercial CDT carbapenemase detection sensitivity for Enterobacterales was 96.49% (86.84-99.39%), and 95.24% (74.13-99.75%) specificity (kappa, 0.90); for Pseudomonas, carbapenemase detection sensitivity was 100.00% (5.46-100.00%) and 37.93% (21.30-57.64%) specificity (kappa, 0.04). When cloxacillin testing was added, CDT specificity reached 84.61% (64.27-94.95%).

Conclusion

The molecular epidemiology of carbapenem-non-susceptible isolates from pediatric patients in Southern China exhibited distinctive characteristics. Both the mCIM-eCIM combination and CDT methods effectively detected and differentiated carbapenemases among Enterobacterales isolates, and the former performed better than CDT among Pseudomonas.

Molecular detection of multidrug and methicillin resistance in Staphylococcus aureus isolated from wild pigeons (Columba livia) in South Africa

Staphylococcus aureus is an important human and veterinary pathogen. The present study aimed to determine the prevalence of antibiotic resistance among S. aureus isolated from samples obtained from free-flying wild pigeons and houseflies from different locations surrounding a local hospital in the Greater Durban area in KwaZulu-Natal Province, South Africa. Environmental fecal samples were obtained from wild pigeons that inhabits the grounds of a local public hospital located on the South Beach area, Durban, South Africa. Housefly samples were collected from three different locations (Kenneth Stainbank Nature Reserve, Montclair/Clairwood, and Glenwood/Berea) in the greater Durban area, all within a close proximity to the hospital. Following enrichment, identification, and antimicrobial resistance profiling, S. aureus isolates were subjected to DNA extraction using the boiling method. It was found that 57 out of 252 samples (22.62%) were positive for S. aureus. The Kirby-Bauer disk diffusion method of antibiotic susceptibility testing was performed and revealed that antibiotic resistance rates to penicillin and rifampicin were the most common, with both returning 48 (84.2%) out of the 57 S. aureus isolates being resistant to penicillin and rifampicin. Antibiotic resistance rates to clindamycin, linezolid, erythromycin, tetracycline, cefoxitin, and ciprofloxacin were 82.5%, 78.9%, 73.7%, 63.2%, 33.3%, and 15.8% respectively. Antibiotic resistance genes were detected using primer-specific PCR and it was found that the prevalence rates of tetM, aac(6')-aph(2″), mecA, tetK, ermc, and blaZ genes were 66.7%, 40.4%, 40.4%, 38.6%, 24.6%, and 3.51% respectively. Statistical analysis revealed significant (p < 0.05) relationships between the tetM, aac(6')-aph(2″), and ermC genes and all parameters tested. A significant correlation between the aac(6')-aph(2″) gene and the tetM (0.506) and ermC (-0.386) genes was identified. It was found that 23 (40.3%) S. aureus isolates were mecA positive, of which 10 (52.6%) out of 19 cefoxitin-resistant isolates were mecA positive and 13 (35.1%) out of 37 cefoxitin-sensitive isolates were mecA positive. The results of the present study demonstrated the detection of methicillin and multidrug resistant S. aureus isolated from samples obtained from wild pigeons and houseflies in the surroundings of a local public hospital in the Greater Durban area in South Africa. The findings of the study may account for the emergence of multidrug-resistant staphylococcal infections. The findings highlight the significant role of wild pigeons and houseflies in the spread of drug-resistant pathogenic S. aureus including MRSA. The conclusions of the present study highlight the improtant role of wildlife and the environment as interconnected contributors of One Health.

Genetic characterization of tetracycline-resistant Staphylococcus aureus with reduced vancomycin susceptibility using whole-genome sequencing

This study aimed to analyze the genetic characteristics of Staphylococcus aureus with reduced vancomycin susceptibility (RVS-SA). Whole-genome sequencing was performed on 27 RVS-SA clinical isolates, and comparative genomic analysis was performed using S. aureus reference strains. Pan-genome orthologous groups (POGs) were identified that were present in RVS-SA but absent in the reference strains, but further analysis showed that the presence of these POGs was influenced by tetracycline resistance rather than vancomycin resistance. Therefore, we restricted our analysis to tetracycline-resistant (tetR) RVS-SA and tetR vancomycin-susceptible S. aureus (VSSA). Phylogenomic analysis showed them to be closely related, and further analysis revealed the presence of an uncharacterized protein SAB0394 and the absence of lytA in tetR RVS-SA, which are involved in cell wall thickening. In summary, using whole-genome sequencing we identified gain or loss of genes in tetR RVS-SA strains. These findings provide insights into the investigation of mechanisms associated with reduced vancomycin susceptibility and have the potential to contribute to the development of molecular biomarkers for the rapid and efficient detection of RVS-SA.

Genomic epidemiology and characterization of Staphylococcus aureus isolates from raw milk in Jiangsu, China: emerging broader host tropism strain clones ST59 and ST398

Staphylococcus aureus is highly pathogenic and can cause disease in both humans and domestic animals. The aim of this study was to investigate the genomic epidemiology of S. aureus isolates from raw milk in Jiangsu Province, China, to identify predominant lineages and their associated genomic and phenotypic characteristics. In this study, we identified 117 S. aureus isolates collected from 1,062 samples in Jiangsu Province between 2021 and 2022. Based on whole-genome sequencing (WGS) data from 117 S. aureus isolates, molecular analyses indicated CC1-ST1 (26.50%, 31/117), CC97-ST97 (18.80%, 22/117), CC398-ST398 (10.26%, 12/117), CC8-ST630 (7.69%, 9/117) and CC59-ST59 (2.56%, 3/117) were the major lineages. The prevalence of mecA-positive strains was 11.11%. Four methicillin-resistant S. aureus (MRSA) lineages were found, including MRSA-ST59-t172 (n = 3), OS-MRSA-ST398-t011 (n = 1), MRSA-ST630-t2196 (n = 2) and OS-MRSA-ST630-t2196 (n = 7). Phenotypic resistance to penicillin (30.77%, 36/117), ciprofloxacin (17.09%, 20/117) and erythromycin (15.38%, 18/117) was observed which corresponded with resistance genotypes. All of the isolates could produce biofilms, and 38.46% (45/117) of isolates had invasion rates in mammary epithelial cells (MAC-T) of greater than 1%. Interestingly, most biofilm-producing and invading isolates harbored ebp-icaA-icaB-icaC-icaR-clfA-clfB-fnbA-fnbB-sdrC-sdrD-sdrE-map-can (27.35%, 32/117) and ebp-icaA-icaB-icaC-icaD-icaR-clfA-clfB-fnbA-fnbB-sdrC-sdrD-sdrE-map (33.33%, 39/117) adherence-associated gene patterns and belonged to lineages CC1 and CC97, respectively. Virulence factor assays showed that 47.01% of the isolates contained at least enterotoxin genes. Isolates harboring the immune evasion cluster (IEC) genes (sea, sak, chp, and scn) were predominantly categorized as STs 464, 398, and 59. IEC-positive ST398 and ST59 isolates contained a very high proportion of virulence genes located on prophages, whereas most IEC-negative ST398 clade isolates carried broad-spectrum drug resistance genes. Meanwhile, the IEC-positive ST398 clade showed a close genetic relationship with isolates from the pork supply chain and hospital surgical site infections. MRSA-ST59 strains showed the closest genetic relationship with an isolate from quick-frozen products. High-risk livestock-associated strains ST398 and MRSA-ST59 were detected in raw milk, indicating a potential public health risk of S. aureus transmission between livestock and humans. Our study highlights the necessity for S. aureus surveillance in the dairy industry.

Phenotypic and genomic characteristics of oxacillin-susceptible mecA-positive Staphylococcus aureus, rapid selection of high-level resistance to beta-lactams

The aim of this study is to describe the phenotypic and genetic properties of oxacillin-susceptible methicillin-resistant Staphylococcus aureus (OS-MRSA) isolates and their beta-lactam resistant derivatives obtained after selection with oxacillin. A collection of hospital- (HA-) and community-acquired (CA-) MRSA was screened for oxacillin susceptibility. Antibiotic susceptibility testing, population analysis profile (PAP), mecA expression analysis, and whole genome sequencing (WGS) were performed for 60 mecA-positive OS-MRSA isolates. Twelve high-level beta-lactam resistant derivatives selected during PAP were also subjected to WGS. OS-MRSA were more prevalent among CA-MRSA (49/205, 24%) than among HA-MRSA (11/575, 2%). OS-MRSA isolates belonged to twelve sequence types (ST), with a predominance of ST22-t223-SCCmec IVc and ST59-t1950-SCCmec V lineages. OS-MRSA were characterized by mecA promoter mutations at - 33 (C→T) or - 7 (G→T/A) along with PBP2a substitutions (S225R or E246G). The basal and oxacillin-induced levels of mecA expression in OS-MRSA isolates were significantly lower than those in control ST8-HA-MRSA isolates. Most of the OS-MRSA isolates were heteroresistant to oxacillin. High-level beta-lactam resistant OS-MRSA derivatives selected with oxacillin carried mutations in mecA auxiliary factors: relA (metabolism of purines), tyrS, cysS (metabolism of tRNAs), aroK, cysE (metabolism of amino acids and glycolysis). Cefoxitin-based tests demonstrated high specificity for OS-MRSA detection. The highest positive predictive values (PPV > 0.95) were observed for broth microdilution, the VITEK® 2 automatic system, and chromogenic media. Susceptibility testing of CA-MRSA requires special attention due to the high prevalence of difficult-to-detect OS-MRSA among them. Mis-prescription of beta-lactams for the treatment of OS-MRSA may lead to selection of high-level resistance and treatment failures.