Novel determination of spa gene diversity and its molecular typing among Staphylococcus aureus Iraqi isolates obtained from different clinical samples

Kareem, Sawsan Mohammed; Al-Jubori, Sawsan Sajid; Ali, Munim Radwan

doi:10.1016/j.nmni.2020.100653

Cited by 11 publications

(12 citation statements)

References 18 publications

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“…The resistance of S. aureus to multiple drugs restricts therapeutic options and causes severe morbidity and mortality in hospitalized patients and among communities (Gajdács 2019). The rate of methicillin resistance in our study was 95.4%, which is comparable with the findings of previous local studies (Al-kadmy 2013; Ibed and Hamim 2014; Kareem et al 2015;Kareem et al 2020) and higher than other studies in different geographic regions of the world (Wang et al 2012;Cirkovic et al 2015;Akanbi et al 2017;Gitau et al 2018). Many factors could contribute to the variation in the rate of resistance, such as the population studied, type of isolates, and prescription of certain antibiotics in different geographic areas.…”

Section: Discussionsupporting

confidence: 91%

“…In Iraq, as indicated in this study and other recent studies (Kareem et al 2015;Kareem et al 2020), the prevalence of MRSA has significantly increased. Therefore, rapid and efficient typing of MRSA isolates is essential for epidemiological survey and infection control.…”

Section: Discussionsupporting

confidence: 80%

“…Recent studies have shown marked dissemination of methicillin-resistant S. aureus in Iraq ( Kareem et al 2015 ; Kareem et al 2020 ). Hence, epidemiological studies of these bacteria are significantly important to determine their source and to control their spread in the community and hospital settings.…”

Section: Introductionmentioning

confidence: 99%

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Spa typing of Staphylococcus aureus Isolated from Clinical Specimens from Outpatients in Iraq

Abdulkareem

Alzaalan

Yaqoob

2021

Polish Journal of Microbiology

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Methicillin-resistant Staphylococcus aureus (MRSA) is notorious as a hospital superbug and a problematic pathogen among communities. The incidence of MRSA has substantially increased over time in Iraq. The aim of this study was to determine the prevalence and spa types of MRSA isolates from outpatients or patients upon admission into hospitals. Various biochemical tests identified S. aureus isolates, and then this identification was confirmed by PCR using species-specific 16S rRNA primer pairs. Antibiotic susceptibility was determined against methicillin, oxacillin, and vancomycin using the disk diffusion method. Vancomycin MIC was detected by VITEK 2 compact system. All the identified isolates were screened for the presence of mecA and lukS-PV-lukF-PV genes; 36 of them were subjected to spa typing-based PCR. Out of 290 clinical samples, 65 (22.4%) were S. aureus, of which 62 (95.4%) strains were resistant to oxacillin and methicillin. Except for two isolates, all MRSA isolates were mecA positive. One of the three MSSA isolates was mecA positive. Five strains were resistant to vancomycin. Fourteen (21.5%) isolates were positive for the presence of lukS-PV-lukF-PV genes. Spa typing of 36 S. aureus isolates revealed eleven different spa types, t304 (30.3%), t307 (19.4%), t346 (8.3%), t044 (8.3%), t15595 (8.3%), t386 (5.5%), t5475 (5.5%), t17928 (2.8%), t14870 (2.8%), t021 (2.8%), and t024 (2.8%). These findings could be useful for assessing the genetic relatedness of strains in the region for epidemiological and monitoring purposes, which would be essential to limiting the spread of MRSA.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionsupporting

confidence: 80%

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Spa typing of Staphylococcus aureus Isolated from Clinical Specimens from Outpatients in Iraq

Abdulkareem

Alzaalan

Yaqoob

2021

Polish Journal of Microbiology

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“…In our laboratory, we use WGS for routine typing and surveillance of MRSA. Here we also included the spa type due to many laboratories still use spa typing as standard method for typing of MRSA even though it lacks of discrimination power in outbreak investigations 25 – 27 .…”

Section: Discussionmentioning

confidence: 99%

Evaluation of within-host evolution of methicillin-resistant Staphylococcus aureus (MRSA) by comparing cgMLST and SNP analysis approaches

Lagos

Sundqvist

Dyrkell

et al. 2022

Sci Rep

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Whole genome sequencing (WGS) of methicillin-resistant Staphylococcus aureus (MRSA) provides high-resolution typing, facilitating surveillance and outbreak investigations. The aim of this study was to evaluate the genomic variation rate in MRSA, by comparing commonly used core genome multilocus sequencing (cgMLST) against single nucleotide polymorphism (SNP) analyses. WGS was performed on 95 MRSA isolates, collected from 20 carriers during years 2003–2019. To assess variation and methodological-related differences, two different cgMLST schemes were obtained using Ridom SeqSphere+ and the cloud-based 1928 platform. In addition, two SNP methods, 1928 platform and Northern Arizona SNP Pipeline (NASP) were used. The cgMLST using Ridom SeqSphere+ and 1928 showed a median of 5.0 and 2.0 allele variants/year, respectively. In the SNP analysis, performed with two reference genomes COL and Newman, 1928 showed a median of 13 and 24 SNPs (including presumed recombination) and 3.8 respectively 4.0 SNPs (without recombination) per individual/year. Accordantly, NASP showed a median of 5.5 and 5.8 SNPs per individual/year. In conclusion, an estimated genomic variation rate of 2.0–5.8 genetic events per year (without recombination), is suggested as a general guideline to be used at clinical laboratories for surveillance and outbreak investigations independently of analysis approach used.

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“…Many of these established techniques are costly and time-consuming, and the discriminatory abilities of these techniques are also different (Du et al 2011 ). However, the spa typing method has been considered as a rapid and inexpensive method for genotyping and it provides high discriminating power than other typing methods (Shittu et al 2011 ; O’Hara et al 2016 ; Goudarzi et al 2017 ; Ali et al 2019 ; Rezai et al 2019 ; Kareem et al 2020 ). Both phenotypic and molecular typing methods have been used widely to detect and differentiate several MRSA strains, but these techniques have certain limitations in infection control and investigating the nosocomial transmission as these techniques provide low resolution and more time-consuming.…”

Section: Introductionmentioning

confidence: 99%

Characterization of methicillin-resistant Staphylococcus aureus through genomics approach

2020

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In the present study, a total of 35 S. aureus isolates collected from two different geographical locations viz., Germany and Hungary were tested for their methicillin-resistant phenotype which revealed a high incidence of methicillin-resistant S. aureus. The quantitative test for biofilm production revealed that 73.3% of isolates were biofilm producers. The isolates were further characterized using a set of biochemical and genotypic methods such as amplification and analysis of S. aureus species-specific sequence and mecA gene. The 33 mecA positive isolates were then characterized by the amplification of SCCmec and pvl toxin genes. Further, based on the biofilm-forming phenotype, 15 isolates were selected and characterized through PCR–RFLP of coa gene, polymorphism of spa gene and amplification of biofilm-associated genes. The dendrogram prepared from the results of both biochemical and genotypic analyses of the 15 isolates showed that except for the isolates SA G5 and SA H29, the rest of the isolates grouped themselves according to their locations. Thus, the two isolates were selected for further characterization through whole-genome sequencing. Comparative genome analysis revealed that SA G5 and SA H29 have 97.20% ANI values with 2344 gene clusters (core-genome) of which 16 genes were related to antibiotic resistance genes and 57 genes encode virulence factors. The highest numbers of singleton genes were found in SA H29 that encodes proteins for virulence, resistance, mobile elements, and lanthionine biosynthesis. The high-resolution phylogenetic trees generated based on shared proteins and SNPs revealed a clear difference between the two strains and can be useful in distinguishing closely related genomes. The present study demonstrated that the whole-genome sequence analysis technique is required to get a better insight into the MRSA strains which would be helpful in improving diagnostic investigations in real-time to improve patient care.

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Novel determination of spa gene diversity and its molecular typing among Staphylococcus aureus Iraqi isolates obtained from different clinical samples

Cited by 11 publications

References 18 publications

Spa typing of Staphylococcus aureus Isolated from Clinical Specimens from Outpatients in Iraq

Spa typing of Staphylococcus aureus Isolated from Clinical Specimens from Outpatients in Iraq

Evaluation of within-host evolution of methicillin-resistant Staphylococcus aureus (MRSA) by comparing cgMLST and SNP analysis approaches

Characterization of methicillin-resistant Staphylococcus aureus through genomics approach

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