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Ghamari M, Jabalameli F, Emaneini M, Beigverdi R. Multiple-locus variable-number tandem repeat analysis for genotyping of erythromycin-resistant group B streptococci in Iran. New Microbes New Infect 2022; 45:100957. [PMID: 35198219 PMCID: PMC8851280 DOI: 10.1016/j.nmni.2022.100957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/26/2021] [Accepted: 01/10/2022] [Indexed: 12/02/2022] Open
Abstract
Background Group B Streptococcus (GBS or S. agalactiae) is an important pathogen causing severe invasive diseases in neonates, pregnant women, and adults with underlying medical conditions. Methods To investigate the incidence of resistance to macrolide, lincosamide and streptogramin type B (MLSB) antibiotics, macrolide and tetracycline resistance determinants and genetic relationships, a total of 146 clinical isolates of GBS were collected from Tehran, Iran. The genetic relationships between erythromycin-resistant strains were determined by multilocus variable tandem repeat analysis (MLVA). Results All isolates were susceptible to penicillin, vancomycin, linezolid, and quinupristin–dalfopristin, but were resistant to tetracycline (96.6%, 141/146), erythromycin (28.1%, 41/146) and clindamycin (16.4%, 24/146). Among the 41 erythromycin-resistant GBS (ERGBS), the most common antimicrobial resistance gene was tetM detected in 92.7% (38/41) of the isolates followed by ermTR and ermB found in 65.8% (27/41) and 29.3% (12/41) of isolates, respectively. Of the 41 ERGBS, 95% (39/41) exhibited the constitutive MLSB phenotype, 2.4% (1/41) displayed inducible MLSB and 2.4% (1/41) had M phenotype. The erm methylase genes were widely related to MLSB phenotype isolates, while the mefA gene was associated with M phenotype. MLVA analysis performed on the 41 ERGBS revealed that 34 MLVA types (MTs). MLVA analysis showed that infections due to ERGBS have been caused by a variety of genotypes, suggesting that ERGBS were clonally unrelated and dissemination of these isolates was not due to a clonal outbreak. Conclusion Careful usage of macrolide antibiotics in therapy, continued surveillance of resistance rate and appropriate infection control measures can help to reduce spreading of resistance isolates.
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Kasela M, Grzegorczyk A, Malm A. Molecular Diversity of Staphylococcus aureus Colonizing the Upper Respiratory Tract of Residents and Staff in A Nursing Home. Pol J Microbiol 2019; 68:371-376. [PMID: 31880882 PMCID: PMC7256757 DOI: 10.33073/pjm-2019-039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/18/2022] Open
Abstract
Elderly people living in nursing homes are a high-risk population for Staphylococcus aureus infection. Multiple comorbidities, a weakened immune system, inadequate hygienic conditions, and crowding might increase the prevalence rates of this opportunistic pathogen. However, the epidemiological aspects, genetic diversity, and transmission of S. aureus in nursing homes are still poorly understood, especially in Poland. This study aimed to determine the genetic relatedness and prevalence of colonization of S. aureus isolated from the anterior nares and the throat of residents and staff in a nursing home located in Lublin, Poland. The study showed a high S. aureus prevalence rate among participants (46.1%), yet there was a low frequency of MRSA strains among residents (1.7%) and staff (0%). The multiple-locus variable-number tandem-repeat fingerprinting (MLVF) analysis demonstrated a high degree of genetic diversity of S. aureus strains colonizing the anterior nares and the throat of the participants. The occurrence of simultaneous colonization with more than one unique S. aureus strain in any one individual as well as the incidence of colonization with the same genetic variant of S. aureus in different individuals was observed. These findings suggest that inter-participant S. aureus transmission might contribute to the development of cross-infections.
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Affiliation(s)
- Martyna Kasela
- Chair and Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin , Lublin , Poland
| | - Agnieszka Grzegorczyk
- Chair and Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin , Lublin , Poland
| | - Anna Malm
- Chair and Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin , Lublin , Poland
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Bengal Bay clone ST772-MRSA-V outbreak: conserved clone causes investigation challenges. J Hosp Infect 2017; 95:253-258. [DOI: 10.1016/j.jhin.2016.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/06/2016] [Indexed: 02/06/2023]
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Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname. Sci Rep 2017; 7:41050. [PMID: 28106148 PMCID: PMC5247709 DOI: 10.1038/srep41050] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/15/2016] [Indexed: 01/20/2023] Open
Abstract
We report the investigation of an outbreak situation of methicillin-resistant Staphylococcus aureus (MRSA) that occurred at the Academic Hospital Paramaribo (AZP) in the Republic of Suriname from April to May 2013. We performed whole genome sequencing with complete gap closure for chromosomes and plasmids on all isolates. The outbreak involved 12 patients and 1 healthcare worker/nurse at the AZP. In total 24 isolates were investigated. spa typing, genome-wide single nucleotide polymorphism (SNP) analysis, ad hoc whole genome multilocus sequence typing (wgMLST), stable core genome MLST (cgMLST) and in silico PFGE were used to determine phylogenetic relatedness and to identify transmission. Whole-genome sequencing (WGS) showed that all isolates were members of genomic variants of the North American USA300 clone. However, WGS revealed a heterogeneous population structure of USA300 circulating at the AZP. We observed up to 8 SNPs or up to 5 alleles of difference by wgMLST when the isolates were recovered from different body sites of the same patient or if direct transmission between patients was most likely. This work describes the usefulness of complete genome sequencing of bacterial chromosomes and plasmids providing an unprecedented level of detail during outbreak investigations not being visible by using conventional typing methods.
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Hosseinkhani F, Jabalameli F, Nodeh Farahani N, Taherikalani M, van Leeuwen WB, Emaneini M. Variable number of tandem repeat profiles and antimicrobial resistance patterns of Staphylococcus haemolyticus strains isolated from blood cultures in children. INFECTION GENETICS AND EVOLUTION 2015; 38:19-21. [PMID: 26656742 DOI: 10.1016/j.meegid.2015.11.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 11/02/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
Abstract
Staphylococcus haemolyticus is a healthcare-associated pathogen and can cause a variety of lifethreatening infections. Additionally, multi-drug resistance (MDR), in particular methicillin-resistant S. haemolyticus (MRSH) isolates, have emerged. Dissemination of such strains can be of great concern in the hospital environment. A total number of 20S. haemolyticus isolates from blood cultures obtained from children were included in this study. A high prevalence of MDR-MRSH isolates with high MIC values to vancomycin was found and 35% of the isolates were intermediate resistant to vancomycin. Multilocus variable number of tandem repeats analysis (MLVF) revealed 5 MLVF types among 20 isolates of S. haemolyticus. Twelve isolates shared the same MLVF type and were isolated from different wards in a pediatric hospital in Iran. This is a serious alarm for infection control; i.e. in the absence of adequate infection diagnostics and infection control guidelines, these resistant strains can spread to other sectors of a hospital and possibly among the community.
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Affiliation(s)
- Faride Hosseinkhani
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fereshteh Jabalameli
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Morovat Taherikalani
- Department of Microbiology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Willem B van Leeuwen
- Department of Innovative Molecular Diagnostics, University of Applied Sciences Leiden, Leiden, The Netherlands
| | - Mohammad Emaneini
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Beigverdi R, Jabalameli F, Mirsalehian A, Hantoushzadeh S, Boroumandi S, Taherikalani M, Emaneini M. Virulence factors, antimicrobial susceptibility and molecular characterization of Streptococcus agalactiae isolated from pregnant women. Acta Microbiol Immunol Hung 2014; 61:425-34. [PMID: 25496971 DOI: 10.1556/amicr.61.2014.4.4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Forty-one Streptococcus agalactiae isolates collected from pregnant women at 35-37 weeks of gestation were analysed for their capsular types, antimicrobial resistance determinants, distribution of virulence factors and genetic relatedness using PCR and multiplex PCR. Capsular type III was predominant (65.8%), followed by capsular type II (14.6%), Ib (7.3%), and V(4.9%). All isolates were susceptible to penicillin, vancomycin, linezolid and quinupristin-dalfopristin. Resistance to tetracycline, erythromycin and clindamycin were found in 97.6%, 24.4%, and 14.6% of isolates, respectively. The most common antimicrobial resistance gene was tetM found in 97.6% of the isolates followed by ermTR and ermB found in 12% and 7.3% of isolates, respectively. The most common virulence gene was hly (100%), followed by scpB (97.6%), bca (97.6%), rib (53.65%) and bac (4.9%). The insertion sequence IS1548 was found in 63.4% of isolates. By multi locus variable number of tandem repeat analysis (MLVA) typing, 30 different allelic profiles or MLVA types (MTs) were identified. The most frequent was the MT1 (5/41, 12.2%) and followed by MT2 (4/41, 9.75%). Our data revealed that population structure of these isolates is highly diverse and indicates different MLVA types.
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Affiliation(s)
- Reza Beigverdi
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Fereshteh Jabalameli
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Akbar Mirsalehian
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Sedigheh Hantoushzadeh
- 2 Tehran University of Medical Sciences Maternal, Fetal and Neonatal Research Center, Vali-asr Hospital Tehran Iran
| | | | - Morovat Taherikalani
- 4 Ilam University of Medical Sciences Clinical Microbiology Research Center Ilam Iran
| | - Mohammad Emaneini
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
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Verhegghe M, Crombé F, Pletinckx LJ, Haesebrouck F, Butaye P, Herman L, Heyndrickx M, Rasschaert G. Genetic diversity of livestock-associated MRSA isolates obtained from piglets from farrowing until slaughter age on four farrow-to-finish farms. Vet Res 2014; 45:89. [PMID: 25217275 PMCID: PMC4189174 DOI: 10.1186/s13567-014-0089-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/08/2014] [Indexed: 01/29/2023] Open
Abstract
During a previous longitudinal study, performed on four farrow-to-finish farms (A to D), samples were taken from twelve sows, their offspring, and the environment on various occasions over six months to study the MRSA presence. During the present study, a selection of the obtained MRSA isolates were typed by multiple-locus variable-number tandem-repeat analysis (MLVA), Pulsed Field Gel Electrophoresis (PFGE), spa typing, and SCCmec typing to study the genetic diversity of LA-MRSA isolates and to determine possible MRSA sources for pig(let)s. PFGE, spa typing, and SCCmec typing revealed the presence of one or few dominant genotype(s) per farm. In contrast, 212 MLVA types were detected on the four farms, forming one cluster on farm A, three on farm B, four on farm C and two on farm D. The genotype, found on farm A was unique for this farm. Farms B, C and D shared one cluster. In general, MLVA types from these clusters were isolated from piglets, sows, and the environment on various sampling events. Piglets carried MLVA types both related and unrelated to their mother sows’ MLVA types at farrowing and onwards. In conclusion, molecular typing revealed that within a farm one or a few dominant strain(s) are widespread. Potential MRSA sources for piglets were mother sows, the environment and other piglets.
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Grzegorczyk A, Malm A. Genotyping of Staphylococcus aureus strains isolated from healthy persistent carriers. Folia Microbiol (Praha) 2014; 59:349-53. [PMID: 24488811 DOI: 10.1007/s12223-013-0294-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 12/10/2013] [Indexed: 10/25/2022]
Abstract
The paper presents results on the relatedness of Staphylococcus aureus strains colonizing the upper respiratory tract isolated from healthy persistent carriers. Genotyping was carried out using two methods--multiple-locus variable-number tandem-repeat fingerprinting (MLVF) and pulsed-field gel electrophoresis (PFGE). By comparison of the results obtained by both methods, good correlations between MLVF and PFGE genotyping of strains isolated from the asymptomatic carriers were observed. Further studies are needed to evaluate methods useful for genotyping of S. aureus strains circulating in the community.
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Affiliation(s)
- Agnieszka Grzegorczyk
- Department of Pharmaceutical Microbiology, Medical University of Lublin, Chodźki 1, 20-093, Lublin, Poland,
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9
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Du XF, Xiao M, Liang HY, Sun Z, Jiang YH, Chen GY, Meng XY, Zou GL, Zhang L, Liu YL, Zhang H, Sun HL, Jiang XF, Xu YC. An improved MLVF method and its comparison with traditional MLVF, spa typing, MLST/SCCmec and PFGE for the typing of methicillin-resistant Staphylococcus aureus. Int J Mol Sci 2014; 15:725-42. [PMID: 24406728 PMCID: PMC3907834 DOI: 10.3390/ijms15010725] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/12/2013] [Accepted: 12/20/2013] [Indexed: 11/16/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has become an important nosocomial pathogen, causing considerable morbidity and mortality. During the last 20 years, a variety of genotyping methods have been introduced for screening the prevalence of MRSA. In this study, we developed and evaluated an improved approach capillary gel electrophoresis based multilocus variable-number tandem-repeat fingerprinting (CGE/MLVF) for rapid MRSA typing. A total of 42 well-characterized strains and 116 non-repetitive clinical MRSA isolates collected from six hospitals in northeast China between 2009 and 2010 were tested. The results obtained by CGE/MLVF against clinical isolates were compared with traditional MLVF, spa typing, Multilocus sequence typing/ staphylococcal cassette chromosome mec (MLST/SCCmec) and pulse field gel electrophoresis (PFGE). The discriminatory power estimated by Simpson's index of diversity was 0.855 (28 types), 0.855 (28 patterns), 0.623 (11 types), 0.517 (8 types) and 0.854 (28 patterns) for CGE/MLVF, traditional MLVF, spa typing, MLST/SCCmec and PFGE, respectively. All methods tested showed a satisfied concordance in clonal complex level calculated by adjusted Rand's coefficient. CGE/MLVF showed better reproducibility and accuracy than traditional MLVF and PFGE methods. In addition, the CGE/MLVF has potential to produce portable results. In conclusion, CGE/MLVF is a rapid and easy to use MRSA typing method with lower cost, good reproducibility and high discriminatory power for monitoring the outbreak and clonal spread of MRSA isolates.
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Affiliation(s)
- Xue-Fei Du
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Meng Xiao
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Hong-Yan Liang
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Zhe Sun
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Yue-Hong Jiang
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Guo-Yu Chen
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Xiao-Yu Meng
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Gui-Ling Zou
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Li Zhang
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Ya-Li Liu
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Hui Zhang
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Hong-Li Sun
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Xiao-Feng Jiang
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Ying-Chun Xu
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
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Rešková Z, Koreňová J, Kuchta T. Effective application of multiple locus variable number of tandem repeats analysis to tracing Staphylococcus aureus in food-processing environment. Lett Appl Microbiol 2013; 58:376-83. [PMID: 24283534 DOI: 10.1111/lam.12200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 11/12/2013] [Accepted: 11/22/2013] [Indexed: 11/27/2022]
Abstract
UNLABELLED A total of 256 isolates of Staphylococcus aureus were isolated from 98 samples (34 swabs and 64 food samples) obtained from small or medium meat- and cheese-processing plants in Slovakia. The strains were genotypically characterized by multiple locus variable number of tandem repeats analysis (MLVA), involving multiplex polymerase chain reaction (PCR) with subsequent separation of the amplified DNA fragments by an automated flow-through gel electrophoresis. With the panel of isolates, MLVA produced 31 profile types, which was a sufficient discrimination to facilitate the description of spatial and temporal aspects of contamination. Further data on MLVA discrimination were obtained by typing a subpanel of strains by multiple locus sequence typing (MLST). MLVA coupled to automated electrophoresis proved to be an effective, comparatively fast and inexpensive method for tracing S. aureus contamination of food-processing factories. SIGNIFICANCE AND IMPACT OF THE STUDY Subspecies genotyping of microbial contaminants in food-processing factories may facilitate identification of spatial and temporal aspects of the contamination. This may help to properly manage the process hygiene. With S. aureus, multiple locus variable number of tandem repeats analysis (MLVA) proved to be an effective method for the purpose, being sufficiently discriminative, yet comparatively fast and inexpensive. The application of automated flow-through gel electrophoresis to separation of DNA fragments produced by multiplex PCR helped to improve the accuracy and speed of the method.
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Affiliation(s)
- Z Rešková
- Department of Microbiology and Molecular Biology, Food Research Institute, Bratislava, Slovakia
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Holmes A, McAllister G, McAdam PR, Hsien Choi S, Girvan K, Robb A, Edwards G, Templeton K, Fitzgerald JR. Genome-wide single nucleotide polymorphism-based assay for high-resolution epidemiological analysis of the methicillin-resistant Staphylococcus aureus hospital clone EMRSA-15. Clin Microbiol Infect 2013; 20:O124-31. [PMID: 23927001 DOI: 10.1111/1469-0691.12328] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 07/04/2013] [Accepted: 07/04/2013] [Indexed: 11/28/2022]
Abstract
The EMRSA-15 clone is a major cause of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) infections in the UK and elsewhere but existing typing methodologies have limited capacity to discriminate closely related strains, and are often poorly reproducible between laboratories. Here, we report the design, development and validation of a genome-wide single nucleotide polymorphism (SNP) typing method and compare it to established methods for typing of EMRSA-15. In order to identify discriminatory SNPs, the genomes of 17 EMRSA-15 strains, selected to represent the breadth of genotypic and phenotypic diversity of EMRSA-15 isolates in Scotland, were determined and phylogenetic reconstruction was carried out. In addition to 17 phylogenetically informative SNPs, five binary markers were included to form the basis of an EMRSA-15 genotyping assay. The SNP-based typing assay was as discriminatory as pulsed-field gel electrophoresis, and significantly more discriminatory than staphylococcal protein A (spa) typing for typing of a representative panel of diverse EMRSA-15 strains, isolates from two EMRSA-15 hospital outbreak investigations, and a panel of bacteraemia isolates obtained in healthcare facilities in the east of Scotland during a 12-month period. The assay is a rapid, and reproducible approach for epidemiological analysis of EMRSA-15 clinical isolates in Scotland. Unlike established methods the DNA sequence-based method is ideally suited for inter-laboratory comparison of identified genotypes, and its flexibility lends itself to supplementation with additional SNPs or markers for the identification of novel S. aureus strains in other regions of the world.
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Affiliation(s)
- A Holmes
- The Roslin Institute and Edinburgh Infectious Diseases, Easter Bush Campus, University of Edinburgh, Edinburgh, UK
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Comparative study of IS6110 restriction fragment length polymorphism and variable-number tandem-repeat typing of Mycobacterium tuberculosis isolates in the Netherlands, based on a 5-year nationwide survey. J Clin Microbiol 2013; 51:1193-8. [PMID: 23363841 DOI: 10.1128/jcm.03061-12] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to switch from IS6110 and polymorphic GC-rich repetitive sequence (PGRS) restriction fragment length polymorphism (RFLP) to 24-locus variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates in the national tuberculosis control program in The Netherlands, a detailed evaluation on discriminatory power and agreement with findings in a cluster investigation was performed on 3,975 tuberculosis cases during the period of 2004 to 2008. The level of discrimination of the two typing methods did not differ substantially: RFLP typing yielded 2,733 distinct patterns compared to 2,607 in VNTR typing. The global concordance, defined as isolates labeled unique or identically distributed in clusters by both methods, amounted to 78.5% (n = 3,123). Of the remaining 855 cases, 12% (n = 479) of the cases were clustered only by VNTR, 7.7% (n = 305) only by RFLP typing, and 1.8% (n = 71) revealed different cluster compositions in the two approaches. A cluster investigation was performed for 87% (n = 1,462) of the cases clustered by RFLP. For the 740 cases with confirmed or presumed epidemiological links, 92% were concordant with VNTR typing. In contrast, only 64% of the 722 cases without an epidemiological link but clustered by RFLP typing were also clustered by VNTR typing. We conclude that VNTR typing has a discriminatory power equal to IS6110 RFLP typing but is in better agreement with findings in a cluster investigation performed on an RFLP-clustering-based cluster investigation. Both aspects make VNTR typing a suitable method for tuberculosis surveillance systems.
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Rapid and high-resolution distinction of community-acquired and nosocomial Staphylococcus aureus isolates with identical pulsed-field gel electrophoresis patterns and spa types. Int J Med Microbiol 2013; 303:70-5. [PMID: 23369304 DOI: 10.1016/j.ijmm.2012.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/26/2012] [Accepted: 12/02/2012] [Indexed: 11/20/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) represent a serious threat for public health worldwide. Of particular concern is the emergence of community-acquired MRSA, which is often difficult to distinguish from nosocomial MRSA due to a lack of suitable typing methods for early detection. For example, the USA300 pulsed-field gel electrophoresis (PFGE) pattern includes both the 'classical' community-acquired USA300 clone with spa type t008 and an epidemiologically unrelated nosocomial clone with spa type t024. Likewise, spa typing cannot distinguish the classic USA300 from nosocomial MRSA with the spa type t008. Since the fast and high-resolution distinction of these S. aureus types is important for infection prevention and surveillance, we investigated whether multiple-locus variable number tandem repeat fingerprinting (MLVF) can be applied to overcome these limitations. Indeed, MLVF correctly grouped 91 MRSA isolates belonging to the classic USA300 lineage, nosocomial MRSA isolates with the USA300 PFGE profile and spa type t024, and nosocomial MRSA isolates with spa type t008 into 3 distinct clusters. Importantly, several sub-clusters were also identified, reflecting epidemiological relationships between the respective isolates. We conclude that MLVF has the discriminatory power needed to rapidly distinguish very similar community-acquired and nosocomial MRSA isolates and that MLVF-based sub-clustering of isolates is highly useful for epidemiological investigations, outbreak prevention, and control.
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Brandt KM, Mellmann A, Ballhausen B, Jenke C, van der Wolf PJ, Broens EM, Becker K, Köck R. Evaluation of multiple-locus variable number of tandem repeats analysis for typing livestock-associated methicillin-resistant Staphylococcus aureus. PLoS One 2013; 8:e54425. [PMID: 23349886 PMCID: PMC3549956 DOI: 10.1371/journal.pone.0054425] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 12/11/2012] [Indexed: 11/30/2022] Open
Abstract
Background The increasing occurrence of livestock-associated (LA) methicillin-resistant Staphylococcus aureus (MRSA) associated with the clonal complex (CC) 398 within the past years shows the importance of standardized and comparable typing methods for the purposes of molecular surveillance and outbreak detection. Multiple-locus variable number of tandem repeats analysis (MLVA) has recently been described as an alternative and highly discriminative tool for S. aureus. However, until now the applicability of MLVA for the typing of LA-MRSA isolates from different geographic origin has not been investigated in detail. We therefore compared MLVA and S. aureus protein A (spa) typing for characterizing porcine MRSA from distinct Dutch and German farms. Methodology/Principal Findings Overall, 134 MRSA isolates originating from 21 different pig-farms in the Netherlands and 36 farms in Germany comprising 21 different spa types were subjected to MLVA-typing. Amplification and subsequent automated fragment sizing of the tandem repeat loci on a capillary sequencer differentiated these 134 isolates into 20 distinct MLVA types. Whereas overall MLVA and spa typing showed the same discriminatory power to type LA-MRSA (p = 0.102), MLVA was more discriminatory than spa typing for isolates associated with the prevalent spa types t011 and t034 (Simpson’s Index of Diversity 0.564 vs. 0.429, respectively; p<0.001). Conclusion Although the applied MLVA scheme was not more discriminatory than spa typing in general, it added valuable information to spa typing results for specific spa types (t011, t034) which are highly prevalent in the study area, i.e. Dutch-German border area. Thus, both methods may complement each other to increase the discriminatory power to resolute highly conserved clones such as CC398 (spa types t011, t034) for the detection of outbreaks and molecular surveillance of zoonotic MRSA.
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Affiliation(s)
- Karin M. Brandt
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | | | - Britta Ballhausen
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Christian Jenke
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | | | - Els M. Broens
- Veterinary Microbiological Diagnostic Centre, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Karsten Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Robin Köck
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- * E-mail:
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Ruffing U, Akulenko R, Bischoff M, Helms V, Herrmann M, von Müller L. Matched-cohort DNA microarray diversity analysis of methicillin sensitive and methicillin resistant Staphylococcus aureus isolates from hospital admission patients. PLoS One 2012; 7:e52487. [PMID: 23285062 PMCID: PMC3527544 DOI: 10.1371/journal.pone.0052487] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 11/13/2012] [Indexed: 12/03/2022] Open
Abstract
As genotyping of S. aureus is important for epidemiologic research and for hygiene management, methods are required for standardized fast and easily applicable evaluation of closely related epidemic strains with high prevalence in hospitals. In this single centre matched control study we compared a new commercially available DNA microarray (IdentiBAC) with standard spa-typing for S. aureus genotyping. Included in the study was a subgroup of 46 MRSA and matched 46 MSSA nasal isolates of the Saarland University Medical Center collected during a state-wide admission prevalence screening. Microarray (MA) and also spa-typing could easily differentiate the genetically diverse MSSA group. However, due to the predominance of CC5/t003 in the MRSA group a sufficient subtyping required analysis of more complex genetic profiles as was shown here by the MA comprising a total number of 334 different hybridization probes. The genetic repertoire of the MRSA group was characterized by more virulence genes as compared to the MSSA group. The standard evaluation of MA results by the original software into CCs, agr-, SCCmec- and capsule-types was substituted in the present study by implementation of multivariate subtyping of closely related CC5 isolates using three different bioinformatic methods (splits graph, cluster dendrogram, and principal component analysis). Each method used was applicable for standardized and highly discriminative subtyping with high concordance. We propose that the identified S. aureus subtypes with characteristic virulence gene profiles are presumably associated also with virulence and pathogenicity in vivo; however, this remains to be analyzed in future studies. MA was superior to spa-typing for epidemiologic and presumably also provide functional respectively virulence associated characterization of S. aureus isolates. This is of specific importance for the hospital setting. In future, MA could become a new standard test for S. aureus typing in combination with multivariate bioinformatic analysis.
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Affiliation(s)
- Ulla Ruffing
- Institute of Medical Microbiology and Hygiene, Saarland University Medical Center, Homburg/Saar, Germany
| | - Ruslan Akulenko
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University Medical Center, Homburg/Saar, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Mathias Herrmann
- Institute of Medical Microbiology and Hygiene, Saarland University Medical Center, Homburg/Saar, Germany
| | - Lutz von Müller
- Institute of Medical Microbiology and Hygiene, Saarland University Medical Center, Homburg/Saar, Germany
- * E-mail:
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Mammina C, Calà C, Bonura C, Di Carlo P, Aleo A, Fasciana T, Giammanco A. Polyclonal non multiresistant methicillin resistant Staphylococcus aureus isolates from clinical cases of infection occurring in Palermo, Italy, during a one-year surveillance period. Ann Clin Microbiol Antimicrob 2012; 11:17. [PMID: 22713430 PMCID: PMC3473248 DOI: 10.1186/1476-0711-11-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 06/05/2012] [Indexed: 11/11/2022] Open
Abstract
Background The evolving epidemiology of methicillin resistant Staphylococcus aureus (MRSA) is characterized by the emergence of infections caused by non multiresistant MRSA carrying staphylococcal chromosomal cassette (SCC)mec IV or V in the healthcare settings. A molecular epidemiological analysis of non multiresistant MRSA isolates from four acute general hospitals was performed in Palermo, Italy, during a one year period. Methods For the purpose of the study, MRSA isolates were defined as non multiresistant when they were susceptible to at least three classes of non β-lactam antibiotics. Seventy-five isolates were submitted to antimicrobial susceptibility testing, multilocus sequence typing (MLST) and polymerase chain reaction (PCR) for SCCmec, accessory gene regulator (agr) groups, arginine catabolic mobile element (ACME) and Panton Valentine leukocidin (PVL) toxin genes. For epidemiological typing, Multiple-Locus Variable-Number Tandem Repeat Fingerprinting (MLVF) was performed on all isolates and pulsed field gel electrophoresis (PFGE) on ST8 isolates. Results Non multiresistant MRSA isolates were isolated from all hospitals. Resistances to ciprofloxacin, macrolides and tetracycline were the most prevalent. MLST attributed 46 isolates with ST22, 13 with ST8, eight with ST1, three with ST50 and three with ST398. SCCmec type IV was found in all isolates. PVL was detected in one ST22 isolate. All isolates tested negative for the ACME element. MLVF identified 31 different patterns, some subtype clusters ranging in size between two and 22 isolates. The closely related PFGE patterns of the ST8 isolates differed from USA300. Conclusions A polyclonal circulation of non multiresistant MRSA along with blurring of boundaries between healthcare associated (HA)-MRSA and community associated (CA)-MRSA appear to be occurring in our epidemiological setting. A better understanding of spread of MRSA with the support of molecular typing can provide invaluable information in the epidemiological, microbiological and clinical fields.
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Affiliation(s)
- Caterina Mammina
- Department of Sciences for Health Promotion G, D'Alessandro, University of Palermo, Palermo, Italy.
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Cavanagh JP, Klingenberg C, Hanssen AM, Fredheim EA, Francois P, Schrenzel J, Flægstad T, Sollid JE. Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis. J Microbiol Methods 2012; 89:159-66. [DOI: 10.1016/j.mimet.2012.03.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/23/2012] [Accepted: 03/23/2012] [Indexed: 10/28/2022]
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Microfluidic-chip-based multiple-locus variable-number tandem-repeat fingerprinting with new primer sets for methicillin-resistant Staphylococcus aureus. J Clin Microbiol 2012; 50:2255-62. [PMID: 22573591 DOI: 10.1128/jcm.00056-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The detection of outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) infections and a rapid and accurate identification of sources and routes of transmission should be conducted in hospital settings as early and swiftly as possible. In this study, we investigated the application potential of a new approach based on multiple-locus variable-number tandem-repeat fingerprinting (MLVF) and microfluidics technology for a rapid discrimination of MRSA lineages in outbreak settings. A total of 206 nonrepetitive MRSA isolates recovered from infected patients at the University Medical Center Groningen between 2000 and 2010 were tested. The results obtained by MLVF using microcapillary electrophoresis with newly designed primers were compared to those obtained by spa typing and multiple-locus variable-number tandem-repeat analysis (MLVA). The discriminatory power was 0.980 (107 patterns), 0.969 (85 allelic profiles), and 0.959 (66 types) for MLVF, MLVA, and spa typing, respectively. All methods tested showed a good concordance of results calculated by the adjusted Rand's coefficient method. Comparisons of data obtained by the three approaches allowed us to propose an 88% cutoff value for the similarity between any two MLVF patterns, which can be used in S. aureus epidemiological studies, including analyses of outbreaks and strain transmission events. Of the three tested methods, MLVF is the cheapest, fastest, and easiest to perform. MLVF applied to microfluidic polymer chips is a rapid, cheap, reproducible, and highly discriminating tool to determine the clonality of MRSA isolates and to trace the spread of MRSA strains over periods of many years. Although spa typing should be used due to its portability of data, MLVF has a high added value because it is more discriminatory.
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van Velzen EVH, Reilly JS, Kavanagh K, Leanord A, Edwards GFS, Girvan EK, Gould IM, Mackenzie FM, Masterton R. A retrospective cohort study into acquisition of MRSA and associated risk factors after implementation of universal screening in Scottish hospitals. Infect Control Hosp Epidemiol 2012; 32:889-96. [PMID: 21828969 DOI: 10.1086/661280] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To estimate the proportion of patients who acquire methicillin-resistant Staphylococcus aureus (MRSA) while in hospital and to identify risk factors associated with acquisition of MRSA. DESIGN Retrospective cohort study. PATIENTS Adult patients discharged from 36 general specialty wards of 2 Scottish hospitals that had implemented universal screening for MRSA on admission. METHODS Patients were screened for MRSA on discharge from hospital by using multisite body swabs that were tested by culture. Discharge screening results were linked to admission screening results. Genotyping was undertaken to identify newly acquired MRSA in MRSA-positive patients on admission. RESULTS Of the 5,155 patients screened for MRSA on discharge, 2.9% (95% confidence interval [CI], 2.43-3.34) were found to be positive. In the subcohort screened on both admission and discharge (n = 2,724), 1.3% of all patients acquired MRSA while in hospital (incidence rate, 2.1/1,000 hospital bed-days in this cohort [95% CI, 1.5-2.9]), while 1.3% remained MRSA positive throughout hospital stay. Three risk factors for acquisition of MRSA were identified: age above 64 years, self-reported renal failure, and self-reported presence of open wounds. On a population level, the prevalence of MRSA colonization did not differ between admission and discharge. CONCLUSIONS Cross-transmission of MRSA takes place in Scottish hospitals that have implemented universal screening for MRSA. This study reinforces the importance of infection prevention and control measures to prevent MRSA cross-transmission in hospitals; universal screening for MRSA on admission will in itself not be sufficient to reduce the number of MRSA colonizations and subsequent MRSA infections.
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Chung S, Yi J, Jang MH, Joo SI, Ra EK, Kim SY, Chang CL, Park SS, Kim EC. Comparison of modified multiple-locus variable-number tandem-repeat fingerprinting with pulsed-field gel electrophoresis for typing clinical isolates of Staphylococcus aureus. Ann Lab Med 2011; 32:50-6. [PMID: 22259779 PMCID: PMC3255498 DOI: 10.3343/alm.2012.32.1.50] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 08/20/2011] [Accepted: 10/12/2011] [Indexed: 11/19/2022] Open
Abstract
Background Multiple-locus variable-number tandem-repeat fingerprinting (MLVF) is based on multiplex PCR, utilizing variable number tandem repeat. Our goal was to compare the performance of MLVF in distinguishing clinical Staphylococcus aureus isolates with that of pulsed-field gel electrophoresis (PFGE), which has traditionally been the gold standard. Methods Sixty-three clinically significant S. aureus isolates were tested using both PFGE and MLVF. Multiplex PCR for MLVF was performed using PCR primers for clfA, clfB, sdrCDE, sspA, and spa. PFGE was performed with genomic DNA fragments generated by SmaI endonuclease digestion. Banding patterns of MLVF or PFGE were analyzed using InfoQuestFP software. Results The hands-on time of our modified method was about 3 h, on average, for each of 18 isolates. PFGE (80% cutoff) or MLVF (75% cutoff) separated all of the 63 isolates into 13 and 12 types, respectively. Three types generated by PFGE were identical to those generated by MLVF. PFGE and MLVF yielded similar Simpson's diversity indices, indicating similar discriminatory power. The overall concordance between PFGE and MLVF was low, as represented by adjusted Rand indices (0.266-0.278). PFGE predicted MLVF type better than MLVF predicted PFGE type, as reflected by Wallace coefficients (PFGE cutoff 80% vs. MLVF cutoff 75%, 0.389 vs. 0.233). Analysis of the relationship between a pair of isolates showed 91.0% concordance between the PFGE (80% cutoff) and MLVF (75% cutoff). Conclusions Our simple, low-cost, modified MLVF protocol can effectively discriminate between S. aureus clinical isolates. MLVF can replace PFGE for the hospital infection control of S. aureus.
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Affiliation(s)
- Soie Chung
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
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From types to trees: reconstructing the spatial spread of Staphylococcus aureus based on DNA variation. Int J Med Microbiol 2011; 301:614-8. [PMID: 21983337 DOI: 10.1016/j.ijmm.2011.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Tracing the spatial spread of pathogens is a key objective of molecular infectious disease epidemiology. Accordingly, a wide range of genotyping approaches have been used to monitor the dissemination of Staphylococcus aureus strains, from localized outbreaks to global spread. We provide a critical review of available methods, revealing that molecular markers currently in use for typing S. aureus acquire changes so slowly that they monitor evolutionary change over timescales that are largely irrelevant to epidemiology. Moreover, the more variable markers frequently do not reflect the pathogen's evolutionary history and, hence, provide potentially misleading information about spread. More recent work has demonstrated that staphylococcal evolution proceeds sufficiently fast that the dynamics of S. aureus spatial spread can be elucidated at great detail on the basis of genome-wide single-nucleotide polymorphisms.
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Everything at once: comparative analysis of the genomes of bacterial pathogens. Vet Microbiol 2011; 153:13-26. [PMID: 21764529 DOI: 10.1016/j.vetmic.2011.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Revised: 06/15/2011] [Accepted: 06/16/2011] [Indexed: 12/12/2022]
Abstract
The sum of unique genes in all genomes of a bacterial species is referred to as the pan-genome and is comprised of variably absent or present accessory genes and universally present core genes. The accessory genome is an important source of genetic variability in bacterial populations, allowing sub-populations of bacteria to better adapt to specific niches. Such subgroups may themselves have a relatively stable core genome that may influence host preference, virulence, or an association with specific disease syndromes. The core genome provides a useful means of phylogenetic reconstruction as well as contributing to phenotypic heterogeneity. Variation within the pan-genome forms the basis of comparative genotyping techniques, which have evolved alongside technology. Current high-throughput sequencing platforms have created an unprecedented opportunity for comparisons among multiple, closely related genomes. The computer algorithms and software for such comparisons continue to evolve and promise exciting advances in the world of bacterial comparative genomics. We review genotyping techniques based upon phenotypic traits, both core and accessory genomes, and look at some of the software programs currently available to perform whole-genome comparative analyses.
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