Antimicrobial Resistance and Molecular Characterization of Staphylococcus aureus Causing Childhood Pneumonia in Shanghai

Prevalence and molecular characteristics of community-associated methicillin-resistant Staphylococcus aureus in the respiratory tracts of Chinese adults with community-acquired pneumonia

BACKGROUND

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is an important pathogen causing healthcare-associated infections. In recent years, an increasing number of CA-MRSA clones have emerged and rapidly spread in the community and hospital settings in China.

OBJECTIVES

To investigate the molecular epidemiology and resistance of CA-MRSA in the respiratory tracts of Chinese adults with community-acquired pneumonia (CAP).

METHODS

A total of 243 sputum samples were collected from adult patients with CAP at the Nantong Hospital in China between 2018 and 2021. S. aureus was identified using PCR, and its susceptibility to 14 antimicrobials was tested using the broth dilution method. Genomic characterization of respiratory CA-MRSA and our previously collected intestinal CA-MRSA isolates was performed using whole-genome sequencing, and the evolutionary relationships of these isolates were assessed using phylogenetic analysis.

RESULTS

The CA-MRSA colonization rate among adults with CAP in China was 7.8 % (19/243). Antimicrobial resistance analysis revealed that the proportion of multidrug-resistant respiratory CA-MRSA isolates (100 %) was higher than that of intestinal CA-MRSA isolates (6.3 %). Among the 35 CA-MRSA isolates, 10 MLST types were identified and clustered into five clone complexes (CCs). CC5 (48.6 %) and CC88 (20 %) were predominant CA-MRSA clones. Notably, the CC5 clone ST764/ST6292-MRSA-II-t002 was identified as the major lineage causing respiratory tract infections in Chinese adults with CAP.

CONCLUSIONS

The prevalence of CA-MRSA among Chinese adults with CAP is high and often involves ST764/ST6292-MRSA-II-t002 as the causal pathogen.

Clinical Characteristics and Microbial Profiles of Paediatric Patients with Methicillin-Resistant Staphylococcus aureus Pneumonia in China

Background: Staphylococcus aureus can cause fatal pneumonia. The evolution of bacteria and the overuse of antibiotics have enhanced the drug resistance of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive Staphylococcus aureus (MSSA). Objectives: This study aimed to recapitulate the microbiological profile and clinical characteristics of paediatric patients with MRSA. Methods: This retrospective study was conducted to investigate 1372 paediatric patients with S. aureus pneumonia from January 2017 to December 2021. Sputum specimens were collected and processed for performing bacterial culture and drug sensitivity tests. Medical records of patients were reviewed for clinical characteristics and laboratory examination results. Results: The MRSA and MSSA pneumonia mainly occurred in infants; however, comparisons of sex, age, and sampling time between patients with MRSA and MSSA pneumonia showed no significant differences (P > 0.05). The results of drug sensitivity in sputum culture revealed that all MRSA and MSSA isolates were susceptible to vancomycin, tigecycline, linezolid, teicoplanin, and ceftaroline. Methicillin-sensitive Staphylococcus aureus was completely sensitive to rifampicin and oxacillin. Methicillin-resistant Staphylococcus aureus was completely resistant to penicillin and oxacillin, while MSSA was less sensitive to penicillin. Methicillin-resistant Staphylococcus aureus and MSSA both maintained high sensitivity rates to gentamicin, sulfamethoxazole-trimethoprim, levofloxacin, and moxifloxacin, with the exception of clindamycin and erythromycin. According to our results, moreover, the sensitivity of MRSA to gentamicin and sulfamethoxazole-trimethoprim was significantly higher than that of MSSA (P < 0.05). The common symptoms of patients with S. aureus pneumonia were fever, cough, and wheezing. patients with MRSA pneumonia had significantly higher counts of white blood cells (WBCs), C-reactive protein (CRP), and procalcitonin (PCT) than patients with MSSA pneumonia (P < 0.05). Conclusions: The results of antimicrobial sensitivity test in sputum culture of MRSA and MSSA isolates can reflect the sensitivity of antibiotics and guide the use of clinical antibiotics. Infectious biomarkers can reflect the severity of infection and guide prognosis.

Antimicrobial resistance profile of methicillin-resistant Staphylococcus aureus isolates in children reported from the ISPED surveillance of bacterial resistance, 2016-2021

Introduction

Methicillin-resistant Staphylococcus aureus (MRSA) poses a serious threat to public health worldwide. In December 2015, the Infectious Disease Surveillance of Pediatrics (ISPED) program was organized to monitor bacterial epidemiology and resistance trends in children.

Methods

This retrospective study was conducted from January 2016-December 2021 on patients at eleven ISPED-group hospitals.

Results

From 2016-2021, a total of 13024 MRSA isolates were obtained from children. The most common age group for patients with MRSA infection was less than 3 years old, and newborns were an important group affected by MRSA infection. MRSA was most commonly isolated from the lower respiratory, an abscess, a secretion, or blood in neonates and from the lower respiratory, an abscess, or the upper respiratory in non-neonates. All isolates were susceptible to vancomycin and linezolid and resistant to penicillin; additionally, 76.88%, 54.97%, 22.30%, 5.67%, 5.14%, 3.63%, and 1.42% were resistant to erythromycin, clindamycin, tetracycline, levofloxacin, sulfamethoxazole-trimethoprim (TMP-SMX), gentamicin, and rifampin, respectively. Between 2016 and 2021, a significant increase was seen in the levofloxacin- and TMP-SMX-resistance rates (from 5.45% to 7.14% and from 4.67% to 6.50%, respectively) among MRSA isolates, along with a significant decrease in the rates of resistance to erythromycin (from 82.61% to 68.08%), clindamycin (from 60.95% to 46.82%), tetracycline (from 25.37% to 17.13%), gentamicin (from 4.53% to 2.82%), and rifampin (from 1.89% to 0.41%).

Discussion

The antibiotic-resistance rates varied among MRSA isolated from different sources. Because of the high antibiotic resistance rate to clindamycin, this antibiotic is not recommended for empirical treatment of MRSA infections, especially in osteomyelitis.

Molecular characterization and virulence gene profiling of methicillin-resistant Staphylococcus aureus associated with bloodstream infections in southern China

Methicillin-resistant Staphylococcus aureus (MRSA) causes an enormous illness burden, including skin and soft tissue infections (SSTIs), pneumonia, bloodstream infections (BSI), and sepsis. BSI are associated with significant patient morbidity and mortality worldwide. However, limited information is available on MRSA-related BSI in China. This study aimed to investigate the molecular characterization of 77 MRSA isolates recovered from hospitalized patients with BSI between 2012 and 2020 at three first-class tertiary hospitals in southern China based on multilocus sequence typing (MLST), spa typing, and staphylococcal cassette chromosome mec (SCCmec) typing. Overall, 13 clonal complexes (CCs) were identified, with CC59 and CC5 being the largest clusters, indicating high genetic diversity among BSI-causing MRSA isolates. ST59 was the most prevalent MLST type (22.1%). ST5/ST764-MRSA SCCmec II was the predominant adult MRSA clone, whereas ST59-MRSA SCCmec IV was the most common pediatric MRSA clone. ST5-t2460, ST764-t1084, and ST59-t437 were the most common types of adult MRSA isolates, whereas ST59-t437 and ST59-t172 were the predominant types of children’s MRSA isolates. ST59-SCCmec IV/V represented the most common clone among community acquired-MRSA isolates. ST5/ST764-SCCmec II was the most common type of hospital-associated MRSA isolate. The most prevalent toxin-encoding genes detected were hla, hld, icaA, and clfA (96.1–100%). Forty-three (100%, 43/43) isolates harbored more than 18 of the tested virulence genes in adults and eight virulence genes (23.5%, 8/34) in children. Virulence gene analysis revealed diversity among different clones: the positivity rates for the Panton-Valentine leukocidin (PVL) gene were 55.8 and 35.3% in adult and pediatric MRSA isolates, respectively; the genes seb–sei were present in all adult strains; seb–seg–sei–seo were present in all ST5, ST59, ST15, ST45, and ST22 adult strains; and seg–sei–sem–sen–seo were present in different clones, including ST15, ST45, and ST22 adult MRSA isolates and ST25, ST30, ST546, and ST72 children’s MRSA isolates. Adult MRSA isolates had significantly higher antibiotic resistance rates and virulence gene prevalence than pediatric MRSA isolates. For 8 years, this study provided epidemiological data on the molecular characteristics and virulence genes in different groups of MRSA BSI in China. Our findings may provide critical information for a better understanding of MRSA BSI.

Prevalence of Livestock-Associated MRSA ST398 in a Swine Slaughterhouse in Guangzhou, China

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is an important zoonotic microorganism that is increasingly causing public health concern worldwide. The objective of this study was to determine the transmission and occurrence of MRSA in a slaughterhouse environment and evaluate its antimicrobial resistance and genetic characterization. In this study, we conducted a comprehensive epidemiological survey of S. aureus by spa typing and whole-genome sequencing (WGS) of samples obtained from the pork production chain, the environment, and community residents. To clarify the evolutionary relationships of MRSA sequence type (ST) 398 in this study and global isolates, 197 published whole-genome sequences data of MRSA ST398 strains were downloaded from the GenBank database and included in the phylogenetic analysis. A total of 585 porcine samples (snout and carcass swabs), 78 human nasal samples, and 136 environmental samples were collected. The MRSA isolates were detected at higher frequencies in samples from swine (15.0%) than carcasses (10.0%), slaughterhouse workers (8.0%), community residents (0%), and environment samples (5.9%). The spa typing results showed that t571 accounted for a higher proportion than other spa types. Closely related isolates from the samples of swine, slaughterhouse workers, carcasses, carrier vehicle, and surrounding fishpond water indicate that MRSA ST398 strains may spread among swine, humans, and the environment. MRSA ST398-t571 isolates were genetically different from global strains, except for two Korean isolates, which showed genetic closeness with it. In addition, a MRSA ST398 isolate recovered from an infected patient in Europe differed by only 31 SNPs from the airborne dust-associated strain isolated in this study, thereby suggesting potential transmission among different countries. Antimicrobial susceptibility testing results demonstrated that 99.0% (96/97) of MRSA and 95.1% (231/243) of methicillin-sensitive S. aureus (MSSA) showed multidrug-resistant (MDR) phenotypes. According to WGS analysis, the poxtA-carrying segment (IS431mec-optrA-IS1216-fexB-IS431mec) was reported in MRSA ST398 isolates for the first time. The coexistence of cfr and optrA in a plasmid was first detected in MRSA ST398. The potential transmission of MRSA among humans, animals, and the environment is a cause for concern. The emergence and transmission of LA-MRSA ST398 with high levels of resistance profiles highlight the urgent need for LA-MRSA surveillance.

Whole-Genome Sequencing and Machine Learning Analysis of Staphylococcus aureus from Multiple Heterogeneous Sources in China Reveals Common Genetic Traits of Antimicrobial Resistance

Staphylococcus aureus is a worldwide leading cause of numerous diseases ranging from food-poisoning to lethal infections. Methicillin-resistant S. aureus (MRSA) has been found capable of acquiring resistance to most antimicrobials. MRSA is ubiquitous and diverse even in terms of antimicrobial resistance (AMR) profiles, posing a challenge for treatment. Here, we present a comprehensive study of S. aureus in China, addressing epidemiology, phylogenetic reconstruction, genomic characterization, and identification of AMR profiles. The study analyzes 673 S. aureus isolates from food as well as from hospitalized and healthy individuals. The isolates have been collected over a 9-year period, between 2010 and 2018, from 27 provinces across China. By whole-genome sequencing, Bayesian divergence analysis, and supervised machine learning, we reconstructed the phylogeny of the isolates and compared them to references from other countries. We identified 72 sequence types (STs), of which, 29 were novel. We found 81 MRSA lineages by multilocus sequence type (MLST), spa, staphylococcal cassette chromosome mec element (SCCmec), and Panton-Valentine leukocidin (PVL) typing. In addition, novel variants of SCCmec type IV hosting extra metal and antimicrobial resistance genes, as well as a new SCCmec type, were found. New Bayesian dating of the split times of major clades showed that ST9, ST59, and ST239 in China and European countries fell in different branches, whereas this pattern was not observed for the ST398 clone. On the contrary, the clonal transmission of ST398 was more intermixed in regard to geographic origin. Finally, we identified genetic determinants of resistance to 10 antimicrobials, discriminating drug-resistant bacteria from susceptible strains in the cohort. Our results reveal the emergence of Chinese MRSA lineages enriched of AMR determinants that share similar genetic traits of antimicrobial resistance across human and food, hinting at a complex scenario of evolving transmission routes. IMPORTANCE Little information is available on the epidemiology and characterization of Staphylococcus aureus in China. The role of food is a cause of major concern: staphylococcal foodborne diseases affect thousands every year, and the presence of resistant Staphylococcus strains on raw retail meat products is well documented. We studied a large heterogeneous data set of S. aureus isolates from many provinces of China, isolated from food as well as from individuals. Our large whole-genome collection represents a unique catalogue that can be easily meta-analyzed and integrated with further studies and adds to the library of S. aureus sequences in the public domain in a currently underrepresented geographical region. The new Bayesian dating of the split times of major drug-resistant enriched clones is relevant in showing that Chinese and European methicillin-resistant S. aureus (MRSA) have evolved differently. Our machine learning approach, across a large number of antibiotics, shows novel determinants underlying resistance and reveals frequent resistant traits in specific clonal complexes, highlighting the importance of particular clonal complexes in China. Our findings substantially expand what is known of the evolution and genetic determinants of resistance in food-associated S. aureus in China and add crucial information for whole-genome sequencing (WGS)-based surveillance of S. aureus.

The Prevalence of Staphylococcus aureus and the Occurrence of MRSA CC398 in Monkey Feces in a Zoo Park in Eastern China

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the important antibiotic resistant pathogens causing infections in humans and animals. The increasing observation of MRSA in wildlife species has raised the concern of its impact on animal health and the potential of zoonotic transmission. This study investigated the prevalence of S. aureus in fecal samples from non-human primates in a zoo located in Jiangsu, China, in which 6 out of 31 (19.4%) fecal samples, and 2 out of 14 (14.3%) indoor room floor swab samples were S. aureus-positive. The antibiotic susceptibility tests of the eight isolates showed that the two isolates were resistant to both penicillin and cefoxitin, the three isolates were resistant only to penicillin, while three isolates were susceptible to all detected antibiotics. The two isolates resistant to cefoxitin were further identified as MRSA by the presence of mecA. Five different spa types were identified including t034 of two MRSA isolates from Trachypithecus francoisi, t189 of two methicillin-susceptible S. aureus (MSSA) isolates from Rhinopithecus roxellana, t377 of two MSSA isolates from Colobus guereza, and two novel spa types t19488 and t19499 from Papio anubis. Whole genome sequencing analysis showed that MRSA t034 isolates belonged to ST398 clustered in clonal complex 398 (CC398) and carried the type B ΦSa3 prophage. The phylogenetic analysis showed that the two MRSA t034/ST398 isolates were closely related to the human-associated MSSA in China. Moreover, two MRSA isolates contained the virulence genes relating to the cell adherence, biofilm formation, toxins, and the human-associated immune evasion cluster, which indicated the potential of bidirectional transfer of MRSA between monkeys and humans. This study is the first to report MRSA CC398 from monkey feces in China, indicating that MRSA CC398 could colonize in monkey and have the risk of transmission between humans and monkeys.

Nasopharyngeal Carriage of Methicillin-Resistant Staphylococcus aureus (MRSA) among Sickle Cell Disease (SCD) Children in the Pneumococcal Conjugate Vaccine Era

The aim of this cross-sectional study was to investigate Staphylococcus aureus nasopharyngeal carriage epidemiology in relation to other nasopharyngeal bacterial colonizers among sickle cell disease (SCD) children about five years into pneumococcal conjugate vaccine 13 (PCV-13) introduction in Ghana. The study involved bacteriological culture of nasopharyngeal swabs obtained from 202 SCD children recruited from the Princess Marie Louise Children's Hospital. S. aureus isolates were identified using standard methods and subjected to antimicrobial susceptibility testing using the Kirby-Bauer disc diffusion method. Cefoxitin-resistant S. aureus isolates were screened for carriage of the mecA, pvl, and tsst-1 genes using multiplex polymerase chain reaction. The carriage prevalence of S. aureus was 57.9% (n = 117), and that of methicillin-resistant S. aureus (MRSA) was 3.5% (n = 7). Carriage of the mecA, pvl, and tsst-1 genes were respectively demonstrated in 20.0% (n = 7), 85.7% (n = 30), and 11.4% (n = 4) of the cefoxitin-resistant S. aureus isolates. PCV-13 vaccination (OR = 0.356, p = 0.004) and colonization with coagulase-negative staphylococci (CoNS) (OR = 0.044, p < 0.0001) each protected against S. aureus carriage. However, none of these and other features of the participants emerged as a determinant of MRSA carriage. The following antimicrobial resistance rates were observed in MRSA compared to methicillin-sensitive S. aureus: clindamycin (28.6% vs. 4.3%), erythromycin (42.9% vs. 19.1%), tetracycline (100% vs. 42.6%), teicoplanin (14.3% vs. 2.6%), penicillin (100% vs. 99.1%), amoxiclav (28.6% vs. 3.5%), linezolid (14.3% vs. 0.0%), ciprofloxacin (42.9% vs. 13.9%), and gentamicin (42.9% vs. 13.0%). The proportion of S. aureus isolates that were multidrug resistant was 37.7% (n = 46). We conclude that S. aureus was the predominant colonizer of the nasopharynx of the SCD children, warranting the continuous monitoring of this risk group for invasive S. aureus infections.

Nasopharyngeal Carriage and Antimicrobial Susceptibility Profile of Staphylococcus aureus among Children under Five Years in Accra

This cross-sectional study investigated the Staphylococcus aureus (S. aureus) and methicillin-resistant S. aureus (MRSA) nasopharyngeal carriage epidemiology in Accra approximately five years post-pneumococcal conjugate vaccines introduction in the country. Archived nasopharyngeal swabs collected from 410 children aged under five years old were bacteriologically cultured. The resultant S. aureus isolates were subjected to antimicrobial susceptibility testing and screening for carriage of the mecA and LukF-PV (pvl) genes, following standard procedures. The data obtained were analyzed with Statistical Products and Services Solutions (SPSS) using descriptive statistics and Chi square tests of associations. The isolated bacteria decreased across coagulase-negative Staphylococci (47.3%, n = 194), S. aureus (23.2%, n = 95), Diphtheroids (5.4%, n = 22), Micrococcus species (3.7%, n = 15), Klebsiella pneumoniae (3.2%, n = 13), Moraxella species and Citrobacter species (1.5% each, n = 6), Escherichia coli, Enterobacter species, and Pseudomonas species (0.9% each, n = 2). The MRSA carriage prevalence was 0.49% (n = 2). Individuals aged 37-48 months recorded the highest proportion of S. aureus carriage (32.6%, 31/95). Resistance of S. aureus to the antibiotics tested were penicillin G (97.9%, n = 93), amoxiclav (20%, n = 19), tetracycline (18.9%, n = 18), erythromycin (5.3%, n = 5), ciprofloxacin (2.1%, n = 2), gentamicin (1.1%, n = 1), cotrimoxazole, clindamycin, linezolid, and teicoplanin (0% each). No inducible clindamycin resistance was observed for the erythromycin-resistant isolates. Three (3.2%) of the isolates were multidrug resistant, of which 66.7% (2/3) were MRSA. The pvl gene was associated with 59.14% (55/93) of the methicillin-sensitive S. aureus (MSSA) isolates, but was not detected among any of the MRSA isolates.

Identification of Methicillin-Resistant Staphylococcus Aureus From Methicillin-Sensitive Staphylococcus Aureus and Molecular Characterization in Quanzhou, China

To distinguish Methicillin-Resistant Staphylococcus aureus (MRSA) from Methicillin-Sensitive Staphylococcus aureus (MSSA) in the protein sequences level, test the susceptibility to antibiotic of all Staphylococcus aureus isolates from Quanzhou hospitals, define the virulence factor and molecular characteristics of the MRSA isolates. MRSA and MSSA Pfam protein sequences were used to extract feature vectors of 188D, n-gram and 400D. Weka software was applied to classify the two Staphylococcus aureus and performance effect was evaluated. Antibiotic susceptibility testing of the 81 Staphylococcus aureus was performed by the Mérieux Microbial Analysis Instrument. The 65 MRSA isolates were characterized by Panton-Valentine leukocidin (PVL), X polymorphic region of Protein A (spa), multilocus sequence typing test (MLST), staphylococcus chromosomal cassette mec (SCCmec) typing. After comparing the results of Weka six classifiers, the highest correctly classified rates were 91.94, 70.16, and 62.90% from 188D, n-gram and 400D, respectively. Antimicrobial susceptibility test of the 81 Staphylococcus aureus: Penicillin-resistant rate was 100%. No resistance to teicoplanin, linezolid, and vancomycin. The resistance rate of the MRSA isolates to clindamycin, erythromycin and tetracycline was higher than that of the MSSAs. Among the 65 MRSA isolates, the positive rate of PVL gene was 47.7% (31/65). Seventeen sequence types (STs) were identified among the 65 isolates, and ST59 was the most prevalent. SCCmec type III and IV were observed at 24.6 and 72.3%, respectively. Two isolates did not be typed. Twenty-one spa types were identified, spa t437 (34/65, 52.3%) was the most predominant type. MRSA major clone type of molecular typing was CC59-ST59-spa t437-IV (28/65, 43.1%). Overall, 188D feature vectors can be applied to successfully distinguish MRSA from MSSA. In Quanzhou, the detection rate of PVL virulence factor was high, suggesting a high pathogenic risk of MRSA infection. The cross-infection of CA-MRSA and HA-MRSA was presented, the molecular characteristics were increasingly blurred, HA-MRSA with typical CA-MRSA molecular characteristics has become an important cause of healthcare-related infections. CC59-ST59-spa t437-IV was the main clone type in Quanzhou, which was rare in other parts of mainland China.

Human Infection of Methicillin-Susceptible Staphylococcus aureus CC398: A Review

Staphylococcus aureus (SA) belonging to the clonal complex 398 (CC398) took a special place within the species due to its spread throughout the world. SA CC398 is broadly separated in two subpopulations: livestock-associated methicillin-resistant SA (MRSA) and human-associated methicillin-susceptible SA (MSSA). Here, we reviewed the global epidemiology of SA CC398 in human clinical infections and focused on MSSA CC398. The last common ancestor of SA CC398 was probably a human-adapted prophage φSa3-positive MSSA CC398 strain, but the multiple transmissions between human and animal made its evolution complex. MSSA and MRSA CC398 had different geographical evolutions. Although MSSA was present in several countries all over the world, it was mainly reported in China and in France with a prevalence about 20%. MSSA CC398 was frequently implicated in severe infections such as bloodstream infections, endocarditis, and bone joint infections whereas MRSA CC398 was mainly reported in skin and soft tissue. The spread of the MSSA CC398 clone is worldwide but with a heterogeneous prevalence. The prophage φSa3 played a crucial role in the adaptation to the human niche and in the virulence of MSSA CC398. However, the biological features that allowed the recent spread of this lineage are still far from being fully understood.

Identification and molecular characterization of Staphylococcus aureus and multi-drug resistant MRSA from monkey faeces in China

Staphylococcus aureus is a commensal bacterium and an important opportunistic pathogen in humans and animals. The increase in multi-drug resistant (MDR) strains of S. aureus is a growing concern due to their impact on animal health and potential for zoonotic transmission. Increasing evidence has shown that MRSA could be transmitted by faeces. The present study determined the prevalence, antibiotic resistance profile and genotypic characteristics of S. aureus isolated from monkey faecal samples in China. Thirty-eight out of 145 (26.21%) macaque faecal samples were S. aureus positive, which eight (5.5%) isolates were identified as MRSA. Antimicrobial susceptibility tests showed that most of the S. aureus isolates were resistant to tetracycline (TE, 44.74%), followed by penicillin (P, 21.05%), cefoxitin (FOX, 21.05%) and ciprofloxacin (CIP, 18.42%). The predominant spa types were t13638 (44.74%) and t189 (13.16%), which are reported to be closely associated with human infections in China. All MRSA isolates belonged to the SCCmecV type, which six of MRSA isolates were ST3268, while the other two isolates belonged to ST4981. This study for the first time describes the prevalence of S. aureus and MRSA in monkey faeces in China, indicating that faeces could be a potential factor of transmitting S. aureus between humans and monkeys.

Genetic diversity and antimicrobial resistance of Staphylococcus aureus from recurrent tonsillitis in children

The aim of this study was to analyze the prevalence of Staphylococcus aureus in the tonsils of children subjected tonsillectomy due to recurrent tonsilitis and to determine the spa types of the pathogens, carriage of virulence genes and antimicrobial resistance profiles. The study included 73 tonsillectomized children. Bacteria, including S. aureus were isolated from tonsillar surface prior to tonsillectomy, recovered from tonsillar core at the time of the surgery, and from posterior pharynx 2-4 weeks after the procedure. Staphylococcus aureus isolates were compared by spa typing, tested for antimicrobial susceptibility and for the presence of superantigenic toxin genes (sea-seu, eta, etb, tst, lukS/lukF-PV) by multiplex polymerase chain reaction. Seventy-three patients (mean 7.1 ± 4.1 years, 61.6% male) were assessed. The most commonly isolated bacteria were S. aureus. The largest proportion of staphylococcal isolates originated from tonsillar core (63%), followed by tonsillar surface (45.1%) and posterior pharynx in tonsillectomized children (18.2%, p = 0.007). Five (6.3%) isolates were identified as MRSA (mecA-positive). Up to 67.5% of the isolates synthesized penicillinases (blaZ-positive isolates), and 8.8% displayed MLS_B resistance. The superantigenic toxin genes were detected in more than half of examined isolates (56.3%). spa types t091, t084, and t002, and clonal complexes (CCs) CC7, CC45, and CC30 turned out to be most common. Staphylococcus aureus associated with RT in children showed pathogenicity potential and considerable genetic diversity, and no clones were found to be specific for this condition although further studies are needed.

Microarray based genetic profiling of Staphylococcus aureus isolated from abattoir byproducts of pork origin

Many parts of pork meat processing are currently not used for human consumption in Switzerland, although they are of great nutritional value. Therefore, data on the occurrence of pathogenic organisms on byproducts is extremely scarce and the prevalence and population structure of Staphylococcus aureus on meat processing sidestreams is unknown. Hence, abattoir byproducts of pork origin including ear, forefoot, heart, intestine, liver, rib bone, sternum, bladder, stomach, hind foot and tongue originating from six abattoirs were screened for S. aureus. The obtained isolates were investigated by spa typing and DNA microarray analysis to reveal their genomic profile and population structure. The prevalence of S. aureus was generally low with a mean of 8%. In total, 40 S. aureus strains were detected and assigned to 12 spa types (t015, t1491, t1778, t091, t337, t899, t2922, t7439, t1333, t208, t4049, t034) and seven clonal complexes (CC1, CC7, CC9, CC30, CC45, CC49, CC398). Detected enterotoxin genes included sea, seb, sec, seh, sel and egc encoded toxin genes seg, sei, sem, sen, seo, and seu. None of the isolates harbored genes conferring methicillin resistance, but blaZ/I/R genes causing penicillin resistance were frequently found. In addition, strains from CC398 exhibited tetM and tetK, conferring tetracycline resistance. Similarity calculations based on microarray profiles revealed no association of clonal complexes with particular body parts, but revealed a certain correspondence of clonal complex and originating abattoir.

Phylogenetic and Molecular Profile of Staphylococcus aureus Isolated from Bloodstream Infections in Northeast Brazil

Staphylococcus aureus is a notorious human pathogen associated with serious nosocomial and community-acquired infections, such as pneumonia, meningitis, endocarditis, toxic shock syndrome, and sepsis, among others. The objective of this study was to investigate the molecular profile, antimicrobial resistance, and clonal diversity of S. aureus isolated from the bloodstream. The determination of the minimum inhibitory concentration (MIC) of the antimicrobial was performed by an automated method. The presence of several virulence and resistance genes was evaluated by PCR. In addition, multilocus sequence typing (MLST) was used to analyze the clonal diversity of S. aureus. A high resistance to oxacillin (78%), clindamycin (78%), erythromycin (70%), ciprofloxacin (61%), and gentamicin (52%) was observed among the isolates. In most of them, the following virulence genes were detected: hlb (83%), ebpS (61%), icaA (57%), fnbpA (17%), and clfA (13%). Only one isolate carried the pvl gene. MLST analysis identified five new sequence types (STs): 5429, 5430, 5431, 5432, and 5433, as well as another seven-ST5, ST97, ST398, ST101, ST30, ST461, and ST2779-among the remaining strains. These seven STs and the four new STs are clustered in four clonal complexes: CC1, CC2, CC7, and CC17. Phylogenetic analysis showed the genetic relationship of the five new ST strains with another 18 strains. Altogether, these analyses indicate the horizontal transfer acquisition of virulence factor genes and multidrug resistance.

Molecular characterization and antimicrobial susceptibility of Staphylococcus aureus isolated from children with acute otitis media in Liuzhou, China

BACKGROUND

There have been few studies focused on the prevalence, bacterial etiology, antibiotic resistance, and genetic background of Staphylococcus aureus (S. aureus) in children with acute otitis media (AOM) in China.

METHODS

A retrospective study was conducted in Liuzhou Maternity and Child Healthcare Hospital. Patients younger than 18 years diagnosed with AOM were enrolled in the study. Middle ear fluid specimens were collected and cultured for bacterial pathogens. The antibiotic susceptibility, virulence genes, macrolide resistant genes and sequence types of S. aureus were identified.

RESULTS

From January 1, 2013 to December 31, 2015, a total of 228 cases of AOM were identified. Pathogenic bacteria were positive in 181 (79.4%) of 228 specimens. Streptococcus pneumoniae was the most common bacteria (36.4%), followed by S. aureus (16.2%). Among the 37 S. aureus isolates, 12 (23.5%) were methicillin-resistant S. aureus (MRSA), and 25 (77.5%) were methicillin-susceptible S. aureus (MSSA). A total of 23 isolates (62.2%) were resistant to erythromycin, 40.5% of isolates were resistant to clindamycin, and 37.8% isolates were resistant to tetracycline. Twenty-three isolates were multi-drug resistant (MDR) S. aureus. Eighteen isolates carried the pvl gene. Up to 22 (59.4%) isolates expressed ermA gene, 8 (21.6%) isolates expressed both ermA and ermC genes, and only 8.1% expressed ermB. Among all S.aureus isolates, 7 sequence types (STs) were identified by multilocus sequence typing (MLST). The most common ST was ST59 (16/37, 43.2%), followed by ST45 (7/37, 18.9%) and ST30 (7/37, 18.9%). The predominant MSSA isolates were ST59-t437-MSSA (5/25, 20.0%), the prevailing MRSA isolates were Taiwan related strains ST59-SCCmec-IVa/V (5/12, 41.6%).

CONCLUSIONS

S. aureus was the second most common cause for AOM in children in Liuzhou. Most of the S. aureus was MDR which carried a high proportion of ermA and ermC gene. CA-MRSA (ST59-SCCmec-IV/V-t437) is circulating in children with AOM. These findings support continued surveillance of S. aureus infections in children with AOM in both communities and hospitals.

Staphylococcus aureus Infecting and Colonizing Experimental Animals, Macaques, in a Research Animal Facility

An outbreak of methicillin-resistant Staphylococcus aureus (MRSA) infections on the skin and soft tissues of experimental macaques in the vivarium of The Rockefeller University, New York, triggered this observational and interventional study. We screened 14 macaques in the colony (samples from head, nares, and rectum) and their housing (40 environmental surfaces) four times in 1 year, for S. aureus colonization or contamination, while implementing enhanced decolonization and decontamination procedures. A total of 114 isolates of S. aureus were recovered and characterized (antibiograms, spa typing, multilocus sequence typing, pulsed-field gel electrophoresis [PFGE], mecA, Panton-Valentine Leukocidin, and arginine catabolic mobile element). Based on these results, six strains of S. aureus were identified: two MRSA strains (t16708/ST3862/PFGE-A, t16709/ST3862/PFGE-C) and one methicillin-sensitive S. aureus (t8397/ST3884/PFGE-D) were characterized for the first time in this study; strains belonging to spa types t189 and t4167 have been identified in primates in previous studies. None of these strains was common to the neighboring New York City human community. Thus, it seems probable that the animals were already colonized upon arrival to the University. We suggest screening primates for S. aureus carriage upon arrival to University vivaria and possible implementation of extensive decolonization procedures before any surgical interventions.

Novel SCCmec type XII methicillin-resistant Staphylococcus aureus isolates identified from a swine production and processing chain

Methicillin-resistant Staphylococcus aureus (MRSA) has been a major public health concern. In this study, a total of 1485 samples from three swine farms, one slaughterhouse and one indoor market in Xiamen, China were collected in 2015, and the prevalence and profiles of MRSA were assessed. All the MRSA isolates were characterized by molecular typing, antibiotic susceptibility, coagulation activity, as well as PCR screening for 38 antibiotic resistance genes, two mobile genetic elements (lsa(E)-containing multiresistance gene cluster and Tn558), and 36 virulence genes. During the study, 54 of 1485 (3.6%) samples from the swine production, processing and retail chain were found positive for MRSA. A relatively rare SCCmecXII genotype was prevalent in swine farm (84.6%, 11/13) and slaughterhouse isolates (80.6%, 25/31), but absent in the market isolates (0%, 0/10). Notably, all staphylococcal cassette chromosome mec (SCCmec) type XII MRSA isolates were resistant to at least 6 classes of antibiotics, carried two mobile genetic elements (lsa(E)-containing multiresistance gene cluster and Tn558) and harbored multiple virulence genes. These multidrug resistant MRSA isolates could also coagulate both bovine and caprine plasma. Our results on the SCCmecXII MRSA isolates, particularly their profiles of related genotypes, antibiotic resistance and virulence determinants, illustrated the evolvement of livestock-associated (LA)-MRSA in the swine production environment and spread along the processing chain. The dominance of the SCCmecXII in MRSA isolates found in this study, differed from previous reports from China, indicated potential contribution associated with the production process.

Molecular characteristics of Staphylococcus aureus isolates from food surveillance in southwest China

BACKGROUND

Staphylococcal food poisoning (SFP) is one of the most common food-borne diseases in the world. Pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and spa typing methods were used to characterize Staphylococcus aureus isolates from food surveillance during 2013-2015 in southwest China, and Staphylococcal cassette chromosome mec (SCCmec) typing was used for methicillin-resistant S. aureus (MRSA). Isolates were also examined for their antibiotic resistance and carriage of virulence genes.

RESULTS

Isolation rate of S. aureus was 2.60% during the three years' surveillance and 29.50% of them were MRSA. All the S. aureus had hla genes (100%), 14.34% of the strains had tst, and 16.73% had PVL. 163 PFGE-SmaI patterns, 41 ST types and 36 spa types were obtained for all the S. aureus. Among them, ST6-t701 (13.15%), ST7-t091 (12.75%), ST59-t437 (9.96%) and ST5-t002 (7.57%) were the prevalent genotypes. Most of MRSA in this study belonged to SCCmec IV and V, accounted for 74.32% and 20.27% respectively. ST6-SCCmec IV-t701 (36.50%) was the most prevalent clone among isolates from food, followed by ST59-SCCmec V-t437 (20.30%), ST5-SCCmec IV-t002 (12.20%) and ST59-SCCmec IV-t437 (12.20%). Some strains had the identical PFGE patterns, ST and spa types with isolates from patients.

CONCLUSIONS

S. aureus isolated from food in southwest China displayed heterogeneity. Isolates had the same genotype profiles with isolates from patients, indicating high homology.

Prevalence, resistance pattern, and molecular characterization of Staphylococcus aureus isolates from healthy animals and sick populations in Henan Province, China

Background

Staphylococcus aureus is one of the most prevalent pathogens and a causative agent of a variety of infections in humans and animals. A total of 640 samples were collected from healthy animals and patients from 2013 to 2014 in Henan Province, China, to investigate the prevalence and perform molecular characterization of S. aureus. Antimicrobial resistance and virulence genes were determined and pulsed-field gel electrophoresis (PFGE) and staphylococcal cassette chromosome mec (SCCmec) typing were performed.

Results

Overall, 22.3% (n = 143) of the samples were positive for S. aureus. The prevalence of methicillin-resistant S. aureus (MRSA) was 5.59%. Capsular polysaccharide locus type 5 (Cap5; 56.64%) was the dominant serotype. S. aureus strains showed high resistance to penicillin (96.50%), ciprofloxacin (52.45%), amikacin (67.83%), erythromycin (96.50%), lincomycin (97.20%), and tetracycline (68.53%) and 109 (76.2%) isolates harbored six or more tested resistance genes. The most predominant resistance genes were aphA (52.45%), ermC (53.15%), and tetM (52.45%). Eighty-seven (60.8%) isolates harbored six or more tested virulence genes. The most predominant enterotoxin genes were sed (20.28%), sej (20.98%), sep (14.69%), and set (37.76%). The prevalence of lukED gene was (57.34%), and a small number of isolates carried pvl (5.59%) and TSST-1 (2.80%). A total of 130 (82.52%) isolates could be typed by PFGE with SmaI digestion. PFGE demonstrated that 45 different patterns (P) that were grouped into 17 pulsotypes and 28 separate pulsotypes using a 90% cut-off value. A total of 118 (82.52%) isolates were successfully typed by spa, and 26 spa types were identified, t15075 (14.00%) and t189 (12.59%) were the most common types. SCCmec types were detected from eight MRSA isolates, with the most prevalent type being SCCmec IVa. MRSA-SCCmec Iva-t437 was observed in human isolates.

Conclusion

This study revealed a high prevalence of S. aureus in healthy animals and patients from Henan Province, China. Resistant S. aureus exhibited varying degrees of multidrug resistance. The presence of antibiotic resistance and virulence genes may facilitate the spread of S. aureus strains and pose a potential threat to public health, highlighting the need for vigilant monitoring of these isolates at the human–animal interface.

Electronic supplementary material

The online version of this article (10.1186/s13099-018-0254-9) contains supplementary material, which is available to authorized users.

Molecular Characteristics of Community-Associated Staphylococcus aureus Isolates From Pediatric Patients With Bloodstream Infections Between 2012 and 2017 in Shanghai, China

Staphylococcus aureus is known as an invasive human pathogen, resulting in significant morbidity and mortality worldwide; however, information on community-associated S. aureus (CA-SA) from bloodstream infections (BSI) in children in China remains scarce. This study aimed to investigate the molecular characteristics of 78 CA-SA isolates recovered from pediatric patients with BSI between 2012 and 2017 in Shanghai. All isolates including 51 (65.4%) methicillin-susceptible S. aureus (MSSA) and 27 (34.6%) methicillin-resistant S. aureus (MRSA) isolates were characterized based on antimicrobial resistance, virulence genes, multilocus sequence typing (MLST), spa, and SCCmec typing. A total of 18 distinct sequence types (STs) and 44 spa types were identified. ST188 and ST7 were the predominant MSSA clones and ST59-MRSA-SCCmecIV/V was the most common MRSA clone. Spa t189 (9.0%, 7/78) was the most common spa type. SCCmec types IV and V were observed at frequencies of 59.3 and 40.7%, respectively. Notably, 40 (51.3%) S. aureus BSI strains were multidrug resistant (MDR), and these were mostly resistant to penicillin, erythromycin, and clindamycin. MRSA strains were associated with substantially higher rates of resistance to multiple antibiotics than MSSA strains. Fifty (64.1%, 50/78) isolates, including 19 (70.3%) MRSA isolates, harbored ≥ 10 tested virulence genes, as evaluated in this study. Ten (37.0%) MRSA isolates and four (7.8%) MSSA isolates harbored the gene encoding Panton-Valentine leukocidin (PVL). Virulence genes analysis showed diversity in different clones; the seb-sek-seq genes were present in all ST59 strains, whereas the seg-sei-sem-sen-seo genes were present in different clones including ST5, ST20, ST22, ST25, ST26, ST30, ST121, and ST487 strains. In conclusion, this study revealed that community-associated S. aureus strains from BSI in children demonstrated considerable genetic diversity, and identified major genotypes of CA-MRSA and CA-MSSA, with a high prevalence of CA-MRSA. Furthermore, major genotypes were frequently associated with specific antimicrobial resistance and toxin gene profiles. Understanding the molecular characteristics of those strains might provide further insights regarding the spread of BSI S. aureus among children between communities in China.

Breast Milk Is a Potential Reservoir for Livestock-Associated Staphylococcus aureus and Community-Associated Staphylococcus aureus in Shanghai, China

Breast milk is the first choice in feeding newborn infants and provides multiple benefits for their growth and development. Staphylococcus aureus usually exists in breast milk and is considered one of the most important causative infective agents. To be effective in preventing and controlling S. aureus infections among infants, the aim of this study was to determine the occurrence and molecular characteristics of S. aureus isolated from 1102 samples of breast milk between 2015 and 2016 in Shanghai, China. Out of 71 S. aureus strains isolated, 15 (21.1%, 15/71) were MRSA and all the strains were characterized by spa typing, Multi-Locus Sequence Typing, SCCmec typing, antibiotic resistance testing and virulence-associated genes. A total of 18 distinct sequence types (STs) and 36 spa types were identified within the 71 isolates, among which the most frequently represented was ST398 (19.7%, 14/71), followed by ST7 (18.3%, 13/71), ST59 (16.9%, 12/71). The three predominant STs accounted for more than one half of all S. aureus isolates. The most prevalent spa types were t091 (12.7%, 9/71), followed by t571 (8.5%, 6/71), t189 (7.0%, 5/71), t034 (5.6%, 4/71), t437 (5.6%, 4/71), and t701 (4.2%, 3/71). All MRSA isolates belonged to SCCmec IV and V, accounting for 66.7 and 33.3% respectively. Notably, 23 (32.4%) S. aureus strains were multidrug resistance (MDR), including 4 (5.6%) MRSA and 19 (26.8%) MSSA strains, and MDR isolates were mostly resistant to penicillin, erythromycin and clindamycin. All isolates exhibited simultaneous carriage of at least 5 of 33 possible virulence genes and the most prevalent genes detected were icaA (100%), clfA (100%), hla (100%), sdrC (94.4%), hlg2 (88.7%), lukE (57.8%). 39 (54.9%, 39/71) isolates, including 9 (12.7%) of MRSA isolates, harbored ≥10 tested virulence genes evaluated in this study. The pvl gene was detected in 8 strains, which represented 5 different STs, with ST59 being the most one. Overall, our findings showed that S. aureus strains isolated from breast milk were mainly MSSA (78.9%, 56/71) and exhibited high genetic diversity in Shanghai area of China. Breast milk was a reservoir for LA-SA (ST398) and CA-SA (ST59), which was likely a vehicle for transmission of multidrug-resistant S. aureus and MRSA lineages. This is a potential public health risk and highlights the need for good hygiene practices to reduce the risk of infant infections.

Prevalence and molecular characterization of Staphylococcus aureus isolated from goats in Chongqing, China

BACKGROUND

Staphylococcus aureus is an important zoonotic pathogen which not only causes significant economic loss in livestock production but also poses a potential threat to public health. Compared with bovine and swine, the information on the colonization of S. aureus in goats is very limited. To understand the prevalence and characteristics of S. aureus in goats, we used the nasal swabs collected from apparently healthy goats to isolate S. aureus, and tested their antimicrobial susceptibility, virulence gene carrying levels, and multilocus sequence typing (MLST).

RESULTS

In 74 nasal swabs of apparently healthy goats, 32 (43.24%) S. aureus strains were isolated and identified, most of which were susceptible to many antibiotics, except for trimethoprim, furazolidone, amoxicillin, lincomycin and roxithromycin, and the resistance incidence of which were 50%, 40.63%, 37.5%, 28.13%, and 21.88% respectively. All the isolates were methicillin-susceptible S. aureus (MSSA) and mecA-negative. Enterotoxin genes were found in 53.13% of the strains. Of which, sej was the most prevalent (21.88%), followed by seb, sec, and see with the same level (18.75%). The most prevalent combination were seb + see and seb + tst. None of the S. aureus isolates harbored sea, sed, seh, eta and etb. Multilocus sequence typing (MLST) revealed 6 new alleles (aroe-552, aroe-553, glpf-500, pta-440, yqil-482 and yqil-496) and 5 new sequence types (STs) (3431,3440,3444,3445 and 3461). Using eBURST, the 5 STs were assigned to clonal complex 522 (CC522) and a further CC with no predicted ancestor. Phylogenetic analysis of seven concatenated MLST alleles revealed that the 5 STs were grouped into cluster I composed of S. aureus mainly from goats and sheep.

CONCLUSION

We provide the data for prevalence of S. aureus in goats in Chongqing municipality and their characterization which will help in tracking evolution of epidemic strains and their control methods.