Molecular Characteristics of Community-Associated Staphylococcus aureus Isolates From Pediatric Patients With Bloodstream Infections Between 2012 and 2017 in Shanghai, China.
ABSTRACT: 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.
Project description:Genomic characterization was conducted on 2 methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) strains isolated from 2 horses hospitalized during an overlapping period of time and 2 methicillin-sensitive <i>S. aureus</i> (MSSA) strains isolated from 2 distinct horses. Phylogenetic proximity was traced and the genotypic and phenotypic characteristics of the antimicrobial resistance of the strains were compared. Whole genome sequencing of MRSA strains for this report was similar but differed from whole genome sequencing of MSSA strains. The MRSA strains were closely related, belonging to sequence type (ST) 612, <i>spa</i> type t1257, and SCC<i>mec</i> type IVd2B. The MSSA strains were also closely related, belonging to ST1660, <i>spa</i> type t3043, and having no detectable staphylococcal cassette chromosome <i>mec</i> elements. All MSRA and MSSA strains were Panton-Valentine leukocidin negative. There were discrepancies in the genotypic analysis and the antimicrobial susceptibility testing (phenotypic analysis) of MRSA strains for rifampin, trimethoprim-sulfamethoxazole, gentamicin, amikacin, and enrofloxacin.
Project description:Methicillin-susceptible Staphylococcus aureus (MSSA) can arise from methicillin-resistant S. aureus (MRSA) following partial or complete excision of staphylococcal cassette chromosome mec (SCCmec). This study investigated whether multiresistant MSSA isolates from Irish hospitals, where MRSA has been endemic for decades, harbor SCCmec DNA. Twenty-five multiresistant MSSA isolates recovered between 2002 and 2006 were tested for SCCmec DNA by PCR and were genotyped by multilocus sequence typing and spa typing. All isolates lacked mecA. Three isolates (12%) harbored SCCmec DNA; two of these (genotype ST8/t190) harbored a 26-kb SCCmec IID (II.3.1.2) remnant that lacked part of mecI and all of mecR1, mecA, and IS431; the third isolate (ST8/t3209) harbored the SCCmec region from dcs to orfX. All three isolates were detected as MRSA using the BD GeneOhm and Cepheid's Xpert MRSA real-time PCR assays. Six isolates (ST8/t190, n = 4; ST5/t088, n = 2), including both isolates with the SCCmec IID remnant, harbored ccrAB4 with 100% identity to ccrAB4 from the Staphylococcus epidermidis composite island SCC-CI. This ccrAB4 gene was also identified in 23 MRSA isolates representative of ST8/t190-MRSA with variant SCCmec II subtypes IIA to IIE, which predominated previously in Irish hospitals. ccrAB4 was located 5,549 bp upstream of the left SCCmec junction in both the MRSA and MSSA isolates with SCCmec elements and remnants and 5,549 bp upstream of orfX in the four MSSA isolates with ccrAB4 only on an SCC-CI homologous region. This is the first description of a large SCCmec remnant with ccr and partial mec genes in MSSA and of the S. epidermidis SCC-CI and ccrAB4 genes in S. aureus.
Project description:Breast milk is the first choice in feeding newborn infants and provides multiple benefits for their growth and development. <i>Staphylococcus aureus</i> usually exists in breast milk and is considered one of the most important causative infective agents. To be effective in preventing and controlling <i>S. aureus</i> infections among infants, the aim of this study was to determine the occurrence and molecular characteristics of <i>S. aureus</i> isolated from 1102 samples of breast milk between 2015 and 2016 in Shanghai, China. Out of 71 <i>S. aureus</i> strains isolated, 15 (21.1%, 15/71) were MRSA and all the strains were characterized by <i>spa</i> typing, Multi-Locus Sequence Typing, SCC<i>mec</i> typing, antibiotic resistance testing and virulence-associated genes. A total of 18 distinct sequence types (STs) and 36 <i>spa</i> 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 <i>S. aureus</i> isolates. The most prevalent <i>spa</i> types were <i>t</i>091 (12.7%, 9/71), followed by <i>t</i>571 (8.5%, 6/71), <i>t</i>189 (7.0%, 5/71), <i>t</i>034 (5.6%, 4/71), <i>t</i>437 (5.6%, 4/71), and <i>t</i>701 (4.2%, 3/71). All MRSA isolates belonged to SCC<i>mec</i> IV and V, accounting for 66.7 and 33.3% respectively. Notably, 23 (32.4%) <i>S. aureus</i> 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 <i>icaA</i> (100%), <i>clfA</i> (100%), <i>hla</i> (100%), <i>sdrC</i> (94.4%), <i>hlg</i>2 (88.7%), <i>lukE</i> (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 <i>pvl</i> gene was detected in 8 strains, which represented 5 different STs, with ST59 being the most one. Overall, our findings showed that <i>S. aureus</i> 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 <i>S. aureus</i> 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.
Project description:OBJECTIVES: Staphylococcus aureus or methicillin-resistant Staphylococcus aureus (MRSA) has been an important pathogen causing bloodstream infections. Our study aimed to investigate the epidemiological and genetic diversity of clinical S. aureus isolates from patients with bloodstream infection in four hospitals of Shanghai from 2009 to 2011. METHODS: A collection of S. aureus isolates causing bloodstream infection from four hospitals in the central part of Shanghai was carried out. Antimicrobial susceptibility testings of collected isolates were performed according to the Clinical and Laboratory Standards Institute (CLSI) guidelines, and spa-type, multi-locus sequence typing, agr type and toxin gene profiling were performed to explore the molecular diversity. Moreover, MRSA strains were also characterized by Staphylococcal cassette chromosome mec (SCCmec) typing. RESULTS: The drugs such as linezolid, teicoplanin and vancomycin were efficacious for treating S. aureus including MRSA bloodstream infection. Methicillin-sensitive Staphylococcus aureus (MSSA) strains displayed distinct diversity in molecular characterization and toxin genes, and three virulent MSSA strains encoding at least five toxins were detected. Five community-associated MRSA (CA-MRSA) strains were found, but the majority (88.7%) of MRSA strains belonged to two epidemic clones (ST239-MRSA- III and ST5-MRSA- II) with different toxin gene profiles among patients with bloodstream infection. CONCLUSIONS: Healthcare-associated MRSA (HA-MRSA) strains were still the main pathogen causing bloodstream infections in spite of the emergence of CA-MRSA strains in hospital setting.
Project description:There has been a worldwide increase in community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) infections. CA-MRSA isolates commonly produce the Panton-Valentine leukocidin toxin encoded by the pvl genes lukF-PV and lukS-PV. This study investigated the clinical and molecular epidemiologies of pvl-positive MRSA and methicillin-susceptible S. aureus (MSSA) isolates identified by the Irish National MRSA Reference Laboratory (NMRSARL) between 2002 and 2011. All pvl-positive MRSA (n=190) and MSSA (n=39) isolates underwent antibiogram-resistogram typing, spa typing, and DNA microarray profiling for multilocus sequence type, clonal complex (CC) and/or sequence type (ST), staphylococcal cassette chromosome mec type assignment, and virulence and resistance gene detection. Where available, patient demographics and clinical data were analyzed. The prevalence of pvl-positive MRSA increased from 0.2% to 8.8%, and that of pvl-positive MSSA decreased from 20% to 2.5% during the study period. The pvl-positive MRSA and MSSA isolates belonged to 16 and 5 genotypes, respectively, with CC/ST8-MRSA-IV, CC/ST30-MRSA-IV, CC/ST80-MRSA-IV, CC1/ST772-MRSA-V, CC30-MSSA, CC22-MSSA, and CC121-MSSA predominating. Temporal shifts in the predominant pvl-positive MRSA genotypes and a 6-fold increase in multiresistant pvl-positive MRSA genotypes occurred during the study period. An analysis of patient data indicated that pvl-positive S. aureus strains, especially MRSA strains, had been imported into Ireland several times. Two hospital and six family clusters of pvl-positive MRSA were identified, and 70% of the patient isolates for which information was available were from patients in the community. This study highlights the increased burden and changing molecular epidemiology of pvl-positive S. aureus in Ireland over the last decade and the contribution of international travel to the influx of genetically diverse pvl-positive S. aureus isolates into Ireland.
Project description:This study investigated the molecular characteristics of rifampin-resistant (RIF-R) <i>Staphylococcus aureus</i> isolates recovered from 4300 retail food samples covering most provincial capitals in China, from 2011 to 2016. Of the 1463 <i>S. aureus</i> enrolled, 149 isolates (142 MSSA and 7 MRSA) were identified as rifampicin-resistant, including 20 high-level (MICs ≥ 8 μg/mL) and 129 low-level (MICs between 2 and 4 μg/mL) rifampicin-resistant strains. Most of the RIF-R <i>S. aureus</i> isolates were resistant to more than three antibiotics. The mutations in the rifampicin resistance-determining region of the <i>rpoB</i> gene were studied in all RIF-R strains. All of the strains presented the mutational change 481 His/Asn and five isolates presented an additional mutation, including 477 Asp/Tyr, 527 Ile/Met, and 466 Leu/Ser, respectively. Thirteen STs and twenty-one <i>spa</i> types were represented, in which five MRSA showed non-type SCC<i>mec</i> and the remaining MRSA belonged to SCC<i>mec</i> type IV-where, ST1-t127 was the predominant type from all of the isolates, while ST398-t034 was the predominant type for the MRSA isolates. In this study, we found that the food-related RIF-R <i>S. aureus</i> may have a unique genetic background selection. However, the scenario regarding the presence of RIF-R <i>S. aureus,</i> especially MRSA, in retail food in China is not favorable and warrants public attention.
Project description:Previous studies have shown that livestock (LA)-MRSA ST398 evolved from a human-adapted methicillin-susceptible <i>S. aureus</i> (MSSA) clone. However, detailed information regarding ST9 is still unclear. Here, we characterized a community-associated methicillin-resistant <i>Staphylococcus aureus</i> (CA-MRSA) ST9-SCC<i>mec</i> XII isolate that has not been previously reported to cause serious disease in China. We obtained whole-genome sequences of one ST9-t899-XII isolate-ZY462471-from a patient with bloodstream infection without livestock contact. The antibiotic susceptibilities of ZY462471 were determined and the clinical information was extracted from medical notes and compared with twenty-seven previously sequenced genomes. Phylogenetic reconstruction was performed to investigate the probable host evolutionary origins of ZY462471, and the difference in resistome and virulence factors were investigated. Virulence assay was performed to evaluate the high virulence potential of ZY462471 and compare the virulence between the closest ST9 MSSA neighbours. Clinical data suggested that ZY462471 is a CA-MRSA. Phylogenetic analysis showed a much closer relationship of ZY462471 with human-associated MSSA ST9 isolates than other LA-MRSA ST9 isolates, suggesting that ZY462471 probably evolved from ST9 MSSA predecessors by acquiring an SCC<i>mec</i> cassette. Importantly, virulence assays indicated that ZY462471 was highly virulent and compared with the MSSA ST9 predecessors, ZY462471 did not show attenuated virulence. Finally, we found that ZY462471 harboured an immune evasion cluster (IEC)-carrying βC-Φ, which is typically found in human clinical <i>S. aureus</i> rather than LA-MRSA isolates, suggesting that ZY4762471 obtained the IEC-carrying βC-Φs from human clinical <i>S. aureus</i> strains. Considering its high virulence potential, this strain should be monitored to prevent more widespread dissemination.
Project description:Here, 210 healthy participants including community personnel (70), clinical students (68), and healthcare workers (HCWs) (72) from the eastern region of Saudi Arabia were studied. Sixty-three <i>Staphylococcus aureus</i> isolates were obtained from the nares of 37% of the community personnel and 26% of the clinical students and HCWs. Methicillin-resistant <i>S. aureus</i> (MRSA) was found in 16% (10 isolates) of the 63 isolates; six were from HCWs. Molecular characterization revealed high clonal diversity among the isolates, with 19 different <i>spa</i> types, 12 clonal complexes (CCs), and seven sequence types (STs) detected. The most common strain type was USA900, CC15, and t084, seen in 11 methicillin-susceptible <i>S. aureus</i> (MSSA) isolates. Moreover, three novel <i>spa</i> types in six isolates and one novel ST in two isolates were identified, most from HCWs. Interestingly, 29 isolates were <i>mec</i>A positive by PCR, whereas only 10 isolates were MRSA by disk diffusion (cefoxitin resistant). Of the 19 MSSA <i>mec</i>A-positive isolates, 16 were PBP2a negative, leaving three unique isolates from HCWs that were <i>mec</i>A and PBP2a positive yet cefoxitin susceptible. Our findings highlight the importance of phenotypically and genotypically characterizing <i>S. aureus</i> strains isolated from healthy communities to monitor the risk of possible cross-transmission to hospitalized patients. The identified strains showed a clonal lineage relationship with previously reported <i>S. aureus</i> and MRSA strains acquired from hospital settings.
Project description:Clonal complex 398 livestok-associated-MRSA (CC398 LA-MRSA) clone is described as a major animal pathogen that can also colonize and infect humans. CC398 methicillin susceptible Staphylococcus aureus (CC398 MSSA) is less described. We identified 126 CC398 MSSA strains of human origin within 6380 S. aureus isolates gathered between 2009 and 2011, from the French National Reference Centre for Staphylococci. They were characterized using antimicrobial susceptibility testing, spa typing, DNA microarrays (Identibac S. aureus Genotyping ®, Alere), CC398-specific sequence PCR, ermT (encoding macrolides résistance) PCR. Fifty-three CC398 LA-MRSA collected from French pigs and veal were used as comparators, and phylogenetic relations between human CC398 MSSA and animal CC398 MRSA populations were explored on the basis of spa-typing and DNA microarrays. CC398 MSSA were able to induce a large spectrum of infections (especially skin, bloodstream, and pneumonias). The prevalence rate of this clone was high in MSSA population, i.e., 24.7% in a local prospective study on nasal colonization, and 7.5% in a national prospective study on infective endocarditis. CC398 MSSA isolates were frequently (89%) erythromycin resistant, due to the presence of the ermT gene, a gene not detected in erythromycin resistant CC398 LA-MRSA strains. Expression of staphylococcal complement inhibitor (scn) and the chemotaxis inhibitory protein (chp), was also specific to this population. The CC398 MRSA signature included also a panel of antibiotic resistance genes, especially a type IV or V cassette mec and tetM. CC398 MSSA and CC398 LA-MRSA populations were closely related based on spa-typing and DNA microarrays, with the MRSA strains forming the most derived lineage in phylogenic trees. Both MSSA and MRSA populations may come from common ancestors, which would have evolved in the settings of different selective pressures, explaining the acquisition of ermT, chp and scn for MSSA, and antibiotic resistance genes for MRSA.
Project description:Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) is mostly found in Thailand in the hospital as a nosocomial pathogen. This study aimed to report the genetic characterization of a clinical community-acquired MRSA (CA-MRSA) isolate collected from hospitalized patients in Thailand. Among 26 MRSA isolates, <i>S. aureus</i> no. S17 preliminarily displayed the presence of a staphylococcal cassette chromosome mec (SCC<i>mec</i>) type IV pattern. The bacterial genomic DNA was subjected to whole-genome sequencing. Panton-Valentine leukocidin (PVL) production, virulence toxins, and antibiotic resistance genes were identified, and multi-locus sequence typing (MLST) and spa typing were performed. The strain was matched by sequence to MLST type 2885 and spa type t13880. This strain carried type IV SCC<i>mec</i> with no PVL production. Five acquired antimicrobial resistance genes, namely <i>blaZ</i>, <i>mecA</i>, <i>Inu(A)</i>, <i>tet(K)</i>, and <i>dfrG</i> conferring resistance to β-lactams, lincosamides, tetracycline, and trimethoprim, were identified. The detected toxins were exfoliative toxin A, gamma-hemolysin, leukocidin D, and leukocidin E. Moreover, there were differences in seven regions in CR-MRSA no. S17 compared to CA-MRSA type 300. In summary, we have reported the ST2885-SCC<i>mec</i> IV CA-MRSA clinical strain in Thailand for the first time, highlighting the problem of methicillin resistance in community settings and the consideration in choosing appropriate antibiotic therapy.