scholarly journals Genomic epidemiology of methicillin-resistant and -susceptible Staphylococcus aureus from bloodstream infections

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Joshua T. Smith ◽  
Elissa M. Eckhardt ◽  
Nicole B. Hansel ◽  
Tahmineh Rahmani Eliato ◽  
Isabella W. Martin ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
New Hampshire ◽  
Resistance Genes ◽  
Bloodstream Infections ◽  
Clonal Expansion ◽  
Recent Common Ancestor ◽  
Methicillin Resistant ◽  
Antimicrobial Resistance Genes ◽  
Hpd Intervals ◽  
Highest Posterior Density

Abstract Background Bloodstream infections due to Staphylococcus aureus cause significant patient morbidity and mortality worldwide. Of major concern is the emergence and spread of methicillin-resistant S. aureus (MRSA) in bloodstream infections, which are associated with therapeutic failure and increased mortality. Methods We generated high quality draft genomes from 323 S. aureus blood culture isolates from patients diagnosed with bloodstream infection at the Dartmouth-Hitchcock Medical Center, New Hampshire, USA in 2010–2018. Results In silico detection of antimicrobial resistance genes revealed that 133/323 isolates (41.18%) carry horizontally acquired genes conferring resistance to at least three antimicrobial classes, with resistance determinants for aminoglycosides, beta-lactams and macrolides being the most prevalent. The most common resistance genes were blaZ and mecA, which were found in 262/323 (81.11%) and 104/323 (32.20%) isolates, respectively. Majority of the MRSA (102/105 isolates or 97.14%) identified using in vitro screening were related to two clonal complexes (CC) 5 and 8. The two CCs emerged in the New Hampshire population at separate times. We estimated that the time to the most recent common ancestor of CC5 was 1973 (95% highest posterior density (HPD) intervals: 1966–1979) and 1946 for CC8 (95% HPD intervals: 1924–1959). The effective population size of CC8 increased until the late 1960s when it started to level off until late 2000s. The levelling off of CC8 in 1968 coincided with the acquisition of SCCmec Type IV in majority of the strains. The plateau in CC8 also coincided with the acceleration in the population growth of CC5 carrying SCCmec Type II in the early 1970s, which eventually leveled off in the early 1990s. Lastly, we found evidence for frequent recombination in the two clones during their recent clonal expansion, which has likely contributed to their success in the population. Conclusions We conclude that the S. aureus population was shaped mainly by the clonal expansion, recombination and co-dominance of two major MRSA clones in the last five decades in New Hampshire, USA. These results have important implications on the development of effective and robust strategies for intervention, control and treatment of life-threatening bloodstream infections.

scholarly journals The First Report of a Methicillin-Resistant Staphylococcus aureus Isolate Harboring Type IV SCCmec in Thailand

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 430
Author(s):  
Wichai Santimaleeworagun ◽  
Praewdow Preechachuawong ◽  
Wandee Samret ◽  
Tossawan Jitwasinkul
Keyword(s):  
Staphylococcus Aureus ◽  
Resistance Genes ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Methicillin Resistance ◽  
Sccmec Type ◽  
Clinical Strain ◽  
Spa Typing ◽  
Methicillin Resistant ◽  
Type Iv ◽  
Antimicrobial Resistance Genes

Methicillin-resistant Staphylococcus aureus (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, S. aureus no. S17 preliminarily displayed the presence of a staphylococcal cassette chromosome mec (SCCmec) 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 SCCmec with no PVL production. Five acquired antimicrobial resistance genes, namely blaZ, mecA, Inu(A), tet(K), and dfrG 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-SCCmec 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.

scholarly journals Species composition and methicillin resistance of staphylococci taken on dairy farms

2020 ◽  
Vol 22 (97) ◽  
pp. 13-19
Author(s):  
Y. V. Horiuk ◽  
M. D. Kukhtyn ◽  
V. Z. Salata ◽  
V. V. Horiuk
Keyword(s):  
Staphylococcus Aureus ◽  
Resistance Genes ◽  
Methicillin Resistance ◽  
Dairy Farms ◽  
Diffusion Method ◽  
Large Reservoir ◽  
Methicillin Resistant ◽  
Antimicrobial Resistance Genes ◽  
Pure Cultures ◽  
Western Ukraine

Methicillin-resistant staphylococci can often asymptomatically colonize animals and humans and are capable of causing disease in them. Therefore, their identification and species identification are important for establishing the source of zoonotic infection and the reservoirs of antimicrobial resistance genes. The purpose of the search was to study the spread of methicillin-resistant staphylococci on dairy farms in the Western region of Ukraine. BD Baird-Parker Agar (HiMedia, India) was used to isolate staphylococci. Specific identification of pure cultures was performed using “RapID Staph Plus” kits (Oxord, UK). Staphylococcus sensitivity to methicillin was determined by inoculum application on Muller-Hinton agar with oxacillin (HiMedia, India). The sensitivity of the isolates to antibacterial preparations was determined by disco-diffusion method. The results of our searches show that Staphylococcus aureus is virtually identical in the amount both from cows (50.1 %) and from humans (62.4 %). In this case the frequency of its isolation among other species was 20.3 %. Along with Staphylococcus aureus there are such species as: S. haemolyticus (20.3 %), S. saprophyticus (13.6 %), S. xylosus (14.0 %), S. chromogenes (11.1 %), S. sciuri (8.8 %), S. epidermidis (4.8 %), S. hominis (3.4 %), S. cohnii (2.6 %) and S. warner (0.7 %). In this case, approximately the same irradiation of cows, humans and the environment by species S. haemolyticus (44.5:70.8:58.8 %), S. epidermidis (12.7:16.6:9.1 %), S. xylosus (26.0:37.4:52.9 %) is observed. The share of S. aureus strains on methicillin-resistant dairy farms in the Western Ukraine is 26.8 %. The proportion of S. aureus strains on methicillin-resistant dairy farms in the Western Ukraine is 26.8 %. Methicillin resistance is also shown S. haemolyticus, S. saprophyticus, S. xylosus та S. chromogenes. In this case their number is 1.1, 1.3, 1.6 and 5.5 times lower, respectively, and S. hominis 1.2 times higher than S. aureus. In addition, the selected cultures simultaneously show resistance to two or more antibiotics. Thus, staphylococci circulating on dairy farms are a large reservoir of resistance genes of antimicrobial preparations. Therefore, it is necessary to establish a constant control of the secretion of staphylococci resistant to β-lactam antibiotics.

scholarly journals Methicillin-Resistant Staphylococcus aureus Clonal Complex 398 as a Major MRSA Lineage in Dogs and Cats in Thailand

Antibiotics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 243
Author(s):  
Surawit Chueahiran ◽  
Jitrapa Yindee ◽  
Pongthai Boonkham ◽  
Nipattra Suanpairintr ◽  
Pattrarat Chanchaithong
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Clonal Complex ◽  
Clinical Samples ◽  
Methicillin Resistant ◽  
Class A ◽  
Antimicrobial Resistance Genes ◽  
Mrsa St398

The aim of this study was to present molecular and antimicrobial resistance characteristics of methicillin-resistant Staphylococcus aureus (MRSA) clonal complex (CC) 398 isolated from diseased dogs and cats in Thailand. A total of 20 MRSA isolates of 134 Staphylococcus aureus isolated from canine and feline clinical samples during 2017–2020 were CC398, consisting of sequence type (ST) 398 (18 isolates), ST5926 (1 isolate), and ST6563 (1 isolate) by multilocus sequence typing. spa t034 and staphylococcal cassette chromosome mec (SCCmec) V were predominantly associated with ST398. Intraclonal differentiation was present by additional spa (t1255, t4653), non-detectable spa, composite SCCmec with a hybrid of ccrA1B1+ccrC and class A mec complex, and DNA fingerprints by pulsed-field gel electrophoresis. The isolates essentially carried antimicrobial resistance genes, mediating multiple resistance to β-lactams (mecA, blaZ), tetracyclines [tet(M)], aminoglycosides [aac(6′)-Ie-aph(2′)-Ia], and trimethoprim (dfr). Livestock-associated MRSA ST398 resistance genes including lnu(B), lsa(E), spw, fexA, and tet(L) were heterogeneously found and lost in subpopulation, with the absence or presence of additional erm(A), erm(B), and ileS2 genes that corresponded to resistance phenotypes. As only a single CC398 was detected with the presence of intraclonal variation, CC398 seems to be the successful MRSA clone colonizing in small animals as a pet-associated MRSA in Thailand.

scholarly journals Novelerm(T)-Carrying Multiresistance Plasmids from Porcine and Human Isolates of Methicillin-Resistant Staphylococcus aureus ST398 That Also Harbor Cadmium and Copper Resistance Determinants

2013 ◽  
Vol 57 (7) ◽  
pp. 3275-3282 ◽  
Author(s):  
Elena Gómez-Sanz ◽  
Kristina Kadlec ◽  
Andrea T. Feßler ◽  
Myriam Zarazaga ◽  
Carmen Torres ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Fold Increase ◽  
Copper Resistance ◽  
Oxidase Gene ◽  
Methicillin Resistant ◽  
Content Type ◽  
Resistance Determinants ◽  
Antimicrobial Resistance Genes

ABSTRACTThis study describes three novelerm(T)-carrying multiresistance plasmids that also harbor cadmium and copper resistance determinants. The plasmids, designated pUR1902, pUR2940, and pUR2941, were obtained from porcine and human methicillin-resistantStaphylococcus aureus(MRSA) of the clonal lineage ST398. In addition to the macrolide-lincosamide-streptogramin B (MLSB) resistance geneerm(T), all three plasmids also carry the tetracycline resistance genetet(L). Furthermore, plasmid pUR2940 harbors the trimethoprim resistance genedfrKand the MLSBresistance geneerm(C), while plasmids pUR1902 and pUR2941 possess the kanamycin/neomycin resistance geneaadD. Sequence analysis of approximately 18.1 kb of theerm(T)-flanking region from pUR1902, 20.0 kb from pUR2940, and 20.8 kb from pUR2941 revealed the presence of several copies of the recently described insertion sequence ISSau10, which is probably involved in the evolution of the respective plasmids. All plasmids carried a functional cadmium resistance operon with the genescadDandcadX, in addition to the multicopper oxidase genemcoand the ATPase copper transport genecopA, which are involved in copper resistance. The comparative analysis ofS. aureusRN4220 and the threeS. aureusRN4220 transformants carrying plasmid pUR1902, pUR2940, or pUR2941 revealed an 8-fold increase in CdSO4and a 2-fold increase in CuSO4MICs. The emergence of multidrug resistance plasmids that also carry heavy metal resistance genes is alarming and requires further surveillance. The colocalization of antimicrobial resistance genes and genes that confer resistance to heavy metals may facilitate their persistence, coselection, and dissemination.

scholarly journals Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections

2021 ◽  
Vol 9 (4) ◽  
pp. 707
Author(s):  
J. Christopher Noone ◽  
Fabienne Antunes Ferreira ◽  
Hege Vangstein Aamot
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Virulence Gene ◽  
Orthopaedic Implant ◽  
Metagenomic Sequencing ◽  
Gene Detection ◽  
Shotgun Metagenomic Sequencing ◽  
Antimicrobial Resistance Genes ◽  
Culture Independent

Our culture-independent nanopore shotgun metagenomic sequencing protocol on biopsies has the potential for same-day diagnostics of orthopaedic implant-associated infections (OIAI). As OIAI are frequently caused by Staphylococcus aureus, we included S. aureus genotyping and virulence gene detection to exploit the protocol to its fullest. The aim was to evaluate S. aureus genotyping, virulence and antimicrobial resistance genes detection using the shotgun metagenomic sequencing protocol. This proof of concept study included six patients with S. aureus-associated OIAI at Akershus University Hospital, Norway. Five tissue biopsies from each patient were divided in two: (1) conventional microbiological diagnostics and genotyping, and whole genome sequencing (WGS) of S. aureus isolates; (2) shotgun metagenomic sequencing of DNA from the biopsies. Consensus sequences were analysed using spaTyper, MLST, VirulenceFinder, and ResFinder from the Center for Genomic Epidemiology (CGE). MLST was also compared using krocus. All spa-types, one CGE and four krocus MLST results matched Sanger sequencing results. Virulence gene detection matched between WGS and shotgun metagenomic sequencing. ResFinder results corresponded to resistance phenotype. S. aureus spa-typing, and identification of virulence and antimicrobial resistance genes are possible using our shotgun metagenomics protocol. MLST requires further optimization. The protocol has potential application to other species and infection types.

scholarly journals Antibiotic Resistance, spa Typing and Clonal Analysis of Methicillin-Resistant Staphylococcus aureus (MRSA) Isolates from Blood of Patients Hospitalized in the Czech Republic

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 395
Author(s):  
Katarina Pomorska ◽  
Vladislav Jakubu ◽  
Lucia Malisova ◽  
Marta Fridrichova ◽  
Martin Musilek ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Czech Republic ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Bloodstream Infections ◽  
Spa Typing ◽  
The Czech Republic ◽  
Methicillin Resistant ◽  
Mrsa Strains ◽  
Spa Types ◽  
Repeat Pattern

Staphylococcus aureus is one of the major causes of bloodstream infections. The aim of our study was to characterize methicillin-resistant Staphylococcus aureus (MRSA) isolates from blood of patients hospitalized in the Czech Republic between 2016 and 2018. All MRSA strains were tested for antibiotic susceptibility, analyzed by spa typing and clustered using a Based Upon Repeat Pattern (BURP) algorithm. The representative isolates of the four most common spa types and representative isolates of all spa clonal complexes were further typed by multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) typing. The majority of MRSA strains were resistant to ciprofloxacin (94%), erythromycin (95.5%) and clindamycin (95.6%). Among the 618 strains analyzed, 52 different spa types were detected. BURP analysis divided them into six different clusters. The most common spa types were t003, t586, t014 and t002, all belonging to the CC5 (clonal complex). CC5 was the most abundant MLST CC of our study, comprising of 91.7% (n = 565) of spa-typeable isolates. Other CCs present in our study were CC398, CC22, CC8, CC45 and CC97. To our knowledge, this is the biggest nationwide study aimed at typing MRSA blood isolates from the Czech Republic.

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