scholarly journals Staphylococcus aureus ST59: Concurrent but Separate Evolution of North American and East Asian Lineages

2021 ◽  
Vol 12 ◽  
Author(s):  
Jo-Ann McClure ◽  
Sahreena Lakhundi ◽  
Amani Niazy ◽  
George Dong ◽  
Osahon Obasuyi ◽  
...  

Despite initially being described in North America, Staphylococcus aureus (SA) sequence type ST59 is the most commonly isolated sequence type in Eastern Asia. The origins and evolution of this strain type remains unclear and therefore we gathered a collection of ST59 isolates from Canada and mainland China for a detailed genetic analysis of the lineage. Bayesian inference phylogenomic analysis of our isolates, along with previously published ST59 sequences indicated that the lineage could be divided into 6 distinct subgroups (WGS-1 thorough 6), each having distinct molecular characteristics. Analysis also demonstrated the concurrent but separate evolution of North American and East Asian lineages, as well as the extensive diversification of the East Asian lineage. The presence of a mobile element structure (MES) was found to be the major difference between these two continental lineages, absent in all North American isolates, and present in all East Asian ones. Other mobile genetic elements, such as the Immune Evasion Complex (IEC), Panton Valentine Leukocidin (PVL), and Staphylococcal Cassette Chromosome mec (SCCmec), showed significant variability within each sub-group and likely represents local selective pressures rather than major characteristics defining the groups. Our analysis also demonstrated the existence of a more ancient ST59 sub-lineage from North America, which was MES negative and contained some of the earliest reported ST59 isolates. Combined with the existence of a MES negative isolate from Taiwan, predicted to have appeared prior to diversification of the East Asian lineages, these results hint at the possibility of a North American origin for the lineage, which gained hold in Eastern Asia following acquisition of MES, and subsequently diversified.

2017 ◽  
Vol 114 (49) ◽  
pp. E10596-E10604 ◽  
Author(s):  
Lena Strauß ◽  
Marc Stegger ◽  
Patrick Eberechi Akpaka ◽  
Abraham Alabi ◽  
Sebastien Breurec ◽  
...  

USA300 is a pandemic clonal lineage of hypervirulent, community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) with specific molecular characteristics. Despite its high clinical relevance, the evolutionary origin of USA300 remained unclear. We used comparative genomics of 224 temporal and spatial diverse S. aureus isolates of multilocus sequence type (ST) 8 to reconstruct the molecular evolution and global dissemination of ST8, including USA300. Analyses of core SNP diversity and accessory genome variations showed that the ancestor of all ST8 S. aureus most likely emerged in Central Europe in the mid-19th century. From here, ST8 was exported to North America in the early 20th century and progressively acquired the USA300 characteristics Panton–Valentine leukocidin (PVL), SCCmec IVa, the arginine catabolic mobile element (ACME), and a specific mutation in capsular polysaccharide gene cap5E. Although the PVL-encoding phage ϕSa2USA was introduced into the ST8 background only once, various SCCmec types were introduced to ST8 at different times and places. Starting from North America, USA300 spread globally, including Africa. African USA300 isolates have aberrant spa-types (t112, t121) and form a monophyletic group within the clade of North American USA300. Large parts of ST8 methicillin-susceptible S. aureus (MSSA) isolated in Africa represent a symplesiomorphic group of ST8 (i.e., a group representing the characteristics of the ancestor), which are rarely found in other world regions. Isolates previously discussed as USA300 ancestors, including USA500 and a “historic” CA-MRSA from Western Australia, were shown to be only distantly related to recent USA300 clones.


2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Xuehan Li ◽  
Tao Huang ◽  
Kai Xu ◽  
Chenglin Li ◽  
Yirong Li

Abstract Background There have been no reports regarding the molecular characteristics, virulence features, and antibiotic resistance profiles of Staphylococcus aureus (S. aureus) from Hainan, the southernmost province of China. Methods Two hundred twenty-seven S. aureus isolates, consisting of 76 methicillin-resistant S. aureus (MRSA) and 151 methicillin-susceptible S. aureus (MSSA), were collected in 2013–2014 and 2018–2019 in Hainan, and investigated for their molecular characteristics, virulence genes, antibiotic resistance profiles and main antibiotic resistance genes. Results Forty sequence types (STs) including three new STs (ST5489, ST5492 and ST5493), and 79 Staphylococcal protein A (spa) types were identified based on multilocus sequence typing (MLST) and spa typing, respectively. ST398 (14.1%, 32/227) was found to be the most prevalent, and the prevalence of ST398-MSSA increased significantly from 2013 to 2014 (5.5%, 5/91) to 2018–2019 (18.4%, 25/136). Seventy-six MRSA isolates were subject to staphylococcus chromosomal cassette mec (SCCmec) typing. SCCmec-IVa was the predominant SCCmec type, and specifically, ST45-SCCmec IVa, an infrequent type in mainland China, was predominant in S. aureus from Hainan. The antibiotic resistance profiles and antibiotic resistance genes of S. aureus show distinctive features in Hainan. The resistant rates of the MRSA isolates to a variety of antibiotics were significantly higher than those of the MSSA isolates. The predominant erythromycin and tetracycline resistance genes were ermC (90.1%, 100/111) and tetK (91.8%, 78/85), respectively. Eleven virulence genes, including the Panton-Valentine leukocidin (pvl) and eta, were determined, and the frequency of eta and pvl were found to be 57.3 and 47.6%. Such high prevalence has never been seen in mainland China before. Conclusion S. aureus isolates in Hainan have unique molecular characteristics, virulence gene and antibiotic resistance profiles, and main antibiotic resistance genes which may be associated with the special geographical location of Hainan and local trends in antibiotic use.


2020 ◽  
Vol 221 (Supplement_2) ◽  
pp. S220-S228 ◽  
Author(s):  
Hongbin Chen ◽  
Yuyao Yin ◽  
Xiaohua Li ◽  
Shuguang Li ◽  
Hua Gao ◽  
...  

Abstract Sequence type (ST) 398 is the most prevalent clone of livestock-associated methicillin-resistant Staphylococcus aureus (MRSA). To evaluate the molecular characteristics and phylogeny of Chinese ST398 isolates, 4 MRSA ST398 strains and 4 methicillin-susceptible S. aureus (MSSA) ST398 strains were collected from patients with bacteremia at 6 teaching hospitals in China between 1999 and 2016. Moreover, 689 ST398 genome sequences were downloaded from the GenBank database for comparison. The 4 MRSA ST398 strains were resistant to β-lactam antibiotics, and 2 strains were also resistant to erythromycin. Among the 4 MSSA ST398 strains, 2 strains displayed multidrug resistance (MDR) and were resistant to penicillin, erythromycin, tetracycline, and gentamicin. The accessory genome of MSSA ST398 was more diverse than that of MRSA ST398. All 4 MRSA ST398 strains carried type V staphylococcal cassette chromosome mec elements; however, MSSA ST398 carried more resistance genes than MRSA ST398. These 4 MRSA ST398 strains carried hemolysin, along with virulence genes associated with immune invasion and protease. Phylogenic analysis showed that the 4 MRSA ST398 strains clustered in 1 clade. The global ST398 phylogeny showed that ST398 was divided into an animal clade and a human clade, and the ST398 strains of this study clustered in the human clade. A small number of human strains were also present in the animal clade and vice versa, suggesting transmission of ST398 between animals and humans. In conclusion, livestock-associated MRSA ST398 has caused severe infections in Chinese hospitals, and it should therefore be paid more attention to and monitored.


2017 ◽  
Vol 49 (6) ◽  
pp. 617-672 ◽  
Author(s):  
John W. SHEARD ◽  
Alexander K. EZHKIN ◽  
Irina A. GALANINA ◽  
Dmitry HIMELBRANT ◽  
Ekaterina KUZNETSOVA ◽  
...  

AbstractRinodinais a widespread, polyphyletic genus of crustosePhysciaceaewithc. 300 species worldwide. A major missing link in understanding its global biogeography has been eastern Asia where the genus has never been systematically revised. Here we review specimen and literature records forRinodinafor north-eastern Asia (Russian Far East, Japan and the Korean Peninsula) and recognize 43 species. We describe two species,R. hypobadiaandR. orientalis, as new to science.Rinodina hypobadiais distinguished by its pigmented hypothecium,Dirinaria-type ascospores and pannarin in both thallus and epihymenium.Rinodina orientalisis characterized by its erumpent apothecia that remain broadly attached, with discs sometimes becoming convex and excluding the thalline margins, ascospores belonging to thePhyscia-type and secondary metabolites absent. Nine other species are reported from the region for the first time. These includeR. dolichospora,R. freyi,R. metaboliza,R. sicula,R. subminutaandR. willeyi. Of particular biogeographical interest are three additional new records that have western North American–eastern Asian distributions: the corticolous speciesR. endospora,R. macrosporaandR. megistospora. Six species have the better known eastern North American–eastern Asian distributions:R. ascociscana(syn.R. akagiensis,R. melancholica),R. buckii,R. chrysidiata,R. subminuta,R. tenuis(syn.R. adirondackii) andR. willeyi, and two have eastern North American–eastern Asian–European distributions:R. excrescensandR. moziana(syn.R. destituta,R. vezdae). Our study begins to close one of the largest gaps in our knowledge of circumboreal species distributions inRinodinaand, together with previous studies in North America and Europe, provides new insights into circumboreal crustose lichen biogeography.Rinodina cinereovirens(syn.R. turfaceavar. cinereovirens) is also reported as new to North America.


2007 ◽  
Vol 52 (3) ◽  
pp. 837-845 ◽  
Author(s):  
Tomomi Takano ◽  
Wataru Higuchi ◽  
Taketo Otsuka ◽  
Tatiana Baranovich ◽  
Shymaa Enany ◽  
...  

ABSTRACTCommunity-acquired methicillin-resistantStaphylococcus aureus(CA-MRSA) strains, which often produce Panton-Valentine leucocidin (PVL), are increasingly noted worldwide. In this study, we examined 42 MRSA strains (25 PVL-positive [PVL+] strains and 17 PVL-negative [PVL−] strains) isolated in Taiwan for their molecular characteristics. The PVL+MRSA strains included CA-MRSA strains with multilocus sequence type (ST) 59 (major PVL+MRSA in Taiwan), its variants, and worldwide CA-MRSA ST30 strains. The PVL−MRSA strains included the pandemic Hungarian MRSA ST239 strain, the Hungarian MRSA ST239 variant, MRSA ST59 (largely hospital-acquired MRSA strains) and its variants, the pandemic New York/Japan MRSA ST5 strain (Japanese type), and the MRSA ST8 strain. The major PVL+CA-MRSA ST59 strain possessed a tetracycline resistance-conferring (tetKpositive) penicillinase plasmid and a drug resistance gene cluster (a possible composite transposon) for multidrug resistance. Moreover, it carried a novel staphylococcal cassette chromosomemec(SCCmec) with two distinctccrCgenes (ccrC2-C8). This SCCmec(previously named SCCmectype VT) was tentatively designated SCCmectype VII. Sequencing of the PVL genes revealed the polymorphisms, and the PVL+CA-MRSA ST59 strain possessed the ST59-specific PVL gene sequence. The data suggest that a significant amount of clonal spread is occurring in Taiwan and that the major PVL+CA-MRSA ST59Taiwanstrain exhibits unique genetic characteristics, such as a novel SCCmectype and an ST59-specific PVL gene sequence.


2001 ◽  
Vol 79 (2) ◽  
pp. 154-169 ◽  
Author(s):  
Félix Forest ◽  
Josée Nadia Drouin ◽  
René Charest ◽  
Luc Brouillet ◽  
Anne Bruneau

The hippocastanaceous Sapindaceae (family Hippocastanaceae) consists of two genera: Aesculus and Billia. The genus Aesculus (buckeyes) is distributed throughout the northern hemisphere. Twelve of the thirteen species of Aesculus are found in eastern Asia and North America, and one is native to Europe. The two species of the genus Billia are found in South and Central America. Aesculus is traditionally divided into five sections. This analysis, based on morphological characters, suggests that the monotypic section Parryanae (Aesculus parryi Gray) is sister to the remainder of the genus, and the other species are divided into two clades. One clade comprises all species from southeastern North America with the monotypic section Macrothyrsus (Aesculus parviflora Walt.) as sister to section Pavia. The other clade consists of all species found in Eurasia included in sections Aesculus and Calothyrsus, with the only North American member of this clade (Aesculus californica (Spach) Nutall) as sister to the rest of the group. According to this analysis, section Calothyrsus is rendered paraphyletic by the inclusion of section Aesculus. In contrast to previous studies that suggest an Asian origin for the genus, our study suggests an American origin for Aesculus from an ancestor similar to Billia with a single migration to Eurasia via the Bering land bridge.Key words: Aesculus, Billia, character evolution, Hippocastanaceae, morphology, phylogeny, Sapindaceae.


2019 ◽  
Author(s):  
Xuehan Li ◽  
Tao Huang ◽  
Kai Xu ◽  
Chenglin Li ◽  
Yirong Li

Abstract Background: There have been no reports regarding the molecular characteristics, virulence features, and antibiotic resistance profiles of Staphylococcus aureus ( S. aureus ) from Hainan, the southernmost province of China. Methods: 227 S. aureus isolates, consisting of 76 methicillin-resistant S. aureus (MRSA) and 151 methicillin-susceptible S. aureus (MSSA), were collected in 2013-2014 and 2018-2019 in Hainan, and investigated for their molecular characteristics, virulence genes, antibiotic resistance profiles and main antibiotic resistance genes. Results: Forty sequence types (STs) including three new STs (ST5489, ST5492 and ST5493), and 79 Staphylococcal protein A ( spa ) types were identified based on multilocus sequence typing (MLST) and spa typing, respectively. ST398 (14.1%, 32/227) was found to be the most prevalent, and the prevalence of ST398-MSSA increased significantly from 2013-2014 (5.5%, 5/91) to 2018-2019 (18.4%, 25/136). Seventy-six MRSA isolates were subject to staphylococcus chromosomal cassette mec (SCC mec ) typing. SCC mec- IVa was the predominant SCC mec type, and specifically, ST45-SCC mec IVa, an infrequent type in mainland China, was predominant in S. aureus from Hainan. The antibiotic resistance profiles and antibiotic resistance genes of S . aureus show distinctive features in Hainan. The resistant rates of the MRSA isolates to a variety of antibiotics were significantly higher than those of the MSSA isolates. The predominant erythromycin and tetracycline resistance genes were ermC (90.1%, 100/111) and tetK (91.8%, 78/85), respectively. Eleven virulence genes, including the Panton-Valentine leukocidin ( pvl ) and eta , were determined, and the frequency of eta and pvl were found to be 57.3% and 47.6%. Such high prevalence has never been seen in mainland China before. Conclusion: S. aureus isolates in Hainan have unique molecular characteristics, virulence gene and antibiotic resistance profiles, and main antibiotic resistance genes which may be associated with the special geographical location of Hainan and local trends in antibiotic use.


2020 ◽  
Vol 11 ◽  
Author(s):  
Fang Wu ◽  
Shou-Jian Li ◽  
Cai-Hong Dong ◽  
Yu-Cheng Dai ◽  
Viktor Papp

The fungus “Fuling” has been used in Chinese traditional medicine for more than 2000 years, and its sclerotia have a wide range of biological activities including antitumour, immunomodulation, anti-inflammation, antioxidation, anti-aging etc. This prized medicinal mushroom also known as “Hoelen” is resurrected from a piece of pre-Linnean scientific literature. Fries treated it as Pachyma hoelen Fr. and mentioned that it was cultivated on pine trees in China. However, this name had been almost forgotten, and Poria cocos (syn. Wolfiporia cocos), originally described from North America, and known as “Tuckahoe” has been applied to “Fuling” in most publications. Although Merrill mentioned a 100 years ago that Asian Pachyma hoelen and North American P. cocos are similar but different, no comprehensive taxonomical studies have been carried out on the East Asian Pachyma hoelen and its related species. Based on phylogenetic analyses and morphological examination on both the sclerotia and the basidiocarps which are very seldomly developed, the East Asian samples of Pachyma hoelen including sclerotia, commercial strains for cultivation and fruiting bodies, nested in a strongly supported, homogeneous lineage which clearly separated from the lineages of North American Wolfiporia cocos and other species. So we confirm that the widely cultivated “Fuling” Pachyma hoelen in East Asia is not conspecific with the North American Wolfiporia cocos. Based on the changes in Art. 59 of the International Code of Nomenclature for algae, fungi, and plants, the generic name Pachyma, which was sanctioned by Fries, has nomenclatural priority (ICN, Art. F.3.1), and this name well represents the economically important stage of the generic type. So we propose to use Pachyma rather than Wolfiporia, and subsequently Pachyma hoelen and Pachyma cocos are the valid names for “Fuling” in East Asia and “Tuckahoe” in North America, respectively. In addition, a new combination, Pachyma pseudococos, is proposed. Furthermore, it seems that Pachyma cocos is a species complex, and that three species exist in North America.


2019 ◽  
Author(s):  
Xuehan Li ◽  
Tao Huang ◽  
Kai Xu ◽  
Chenglin Li ◽  
Yirong Li

Abstract Background: There have been no reports regarding the molecular characteristics, virulence features, and antibiotic resistance profiles of Staphylococcus aureus ( S. aureus ) from Hainan, the southernmost province of China. Methods: 227 S. aureus isolates, consisting of 76 methicillin-resistant S. aureus (MRSA) and 151 methicillin-susceptible S. aureus (MSSA), were collected in 2013-2014 and 2018-2019 in Hainan, and investigated for their molecular characteristics, virulence genes, antibiotic resistance profiles and main antibiotic resistance genes. Results: Forty sequence types (STs) including three new STs (ST5489, ST5492 and ST5493), and 79 Staphylococcal protein A ( spa ) types were identified based on multilocus sequence typing (MLST) and spa typing, respectively. ST398 (14.1%, 32/227) was found to be the most prevalent, and the prevalence of ST398-MSSA increased significantly from 2013-2014 (5.5%, 5/91) to 2018-2019 (18.4%, 25/136). Seventy-six MRSA isolates were subject to staphylococcus chromosomal cassette mec (SCC mec ) typing. SCC mec- IVa was the predominant SCC mec type, and specifically, ST45-SCC mec IVa, an infrequent type in mainland China, was predominant in S. aureus from Hainan. The antibiotic resistance profiles and antibiotic resistance genes of S . aureus show distinctive features in Hainan. The resistant rates of the MRSA isolates to a variety of antibiotics were significantly higher than those of the MSSA isolates. The predominant erythromycin and tetracycline resistance genes were ermC (90.1%, 100/111) and tetK (91.8%, 78/85), respectively. Eleven virulence genes, including the Panton-Valentine leukocidin ( pvl ) and eta , were determined, and the frequency of eta and pvl were found to be 57.3% and 47.6%. Such high prevalence has never been seen in mainland China before. Conclusion: S. aureus isolates in Hainan have unique molecular characteristics, virulence gene and antibiotic resistance profiles, and main antibiotic resistance genes which may be associated with the special geographical location of Hainan and local trends in antibiotic use.


1997 ◽  
Vol 75 (12) ◽  
pp. 2108-2116 ◽  
Author(s):  
Qiuxin Wu ◽  
Gregory M. Mueller

Eastern North America and temperate eastern Asia reportedly share a relatively high number of taxa of macrofungi (mushrooms and relatives), including a number of taxa that have putative eastern North America – temperate eastern Asia disjunct distributions. These reports have been used to imply an affinity between the mycota (fungal equivalent of flora and fauna) of the two regions. To date, however, this affinity has not been examined in detail. A comparison of north temperate macrofungal mycotas was undertaken to examine the similarity between these regions. We used two methods in this study: (i) direct comparison of taxon lists and (ii) calculation of the Simpson Coefficient of similarity from lists of selected taxa. These analyses were based on field work, herbarium records, and published taxonomic treatments for Amanita, Lactarius, Ramaria, and Boletaceae. Results of these analyses document that taxonomic similarity between eastern North America and temperate eastern Asia mycotas can be quite high. In all cases, the calculated similarity values for eastern North America – temperate eastern Asia comparisons are higher than those between either region of North America and Europe or between western North America and eastern Asia. Furthermore, the eastern North American and temperate eastern Asian disjunct distributions of macrofungi are usually limited to the level of species or lower. Key words: biogeography, China, disjunct distribution, macrofungi, North America, Simpson Coefficient.


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