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Rio-Tinto A, Costa NS, Alvim DCSS, Oliveira LMA, De Oliveira TLR, Dos Santos KRN, Fracalanzza SEL, Teixeira LM, Marinho P, Taylor S, Thomas S, Pinto TCA. Increase in methicillin-resistant Staphylococcus spp. colonization among pregnant individuals during COVID-19 pandemic. Sci Rep 2024; 14:14961. [PMID: 38942787 PMCID: PMC11213943 DOI: 10.1038/s41598-024-64422-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/09/2024] [Indexed: 06/30/2024] Open
Abstract
Methicillin-resistant Staphylococcus (MRS) has been associated with neonatal infections, with colonization of the anovaginal tract being the main source of vertical transmission. The COVID-19 pandemic has altered the frequency of antibiotic usage, potentially contributing to changes in the dynamics of bacterial agents colonizing humans. Here we determined MRS colonization rates among pregnant individuals attending a single maternity in Rio de Janeiro, Brazil before (January 2019-March 2020) and during (May 2020-March 2021) the COVID-19 pandemic. Anovaginal samples (n = 806 [521 samples before and 285 during the pandemic]) were streaked onto chromogenic media. Colonies were identified by MALDI-TOF MS. Detection of mecA gene and SCCmec typing were assessed by PCR and antimicrobial susceptibility testing was done according to CLSI guidelines. After the onset of the pandemic, MRS colonization rates increased significantly (p < 0.05) from 8.6% (45) to 54.7% (156). Overall, 215 (26.6%) MRS isolates were detected, of which S. haemolyticus was the most prevalent species (MRSH, 84.2%; 181 isolates). SCCmec type V was the most frequent among MRS (63.3%; 136), and 31.6% (68) of MRS strains had a non-typeable SCCmec, due to new combinations of ccr and mecA complexes. Among MRS strains, 41.9% (90) were resistant to at least 3 different classes of antimicrobial agents, and 60% (54) of them were S. haemolyticus harboring SCCmec V. MRS colonization rates and the emergence of multidrug-resistant variants detected in this study indicate the need for continuing surveillance of this important pathogen within maternal and child populations.
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Affiliation(s)
- A Rio-Tinto
- Instituto de Microbiologia Paulo De Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro-RJ, Brazil.
| | - N S Costa
- Instituto de Microbiologia Paulo De Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro-RJ, Brazil
| | - D C S S Alvim
- Instituto de Microbiologia Paulo De Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro-RJ, Brazil
| | - L M A Oliveira
- Instituto de Microbiologia Paulo De Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro-RJ, Brazil
| | - T L R De Oliveira
- Instituto de Microbiologia Paulo De Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro-RJ, Brazil
| | - K R N Dos Santos
- Instituto de Microbiologia Paulo De Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro-RJ, Brazil
| | - S E L Fracalanzza
- Instituto de Microbiologia Paulo De Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro-RJ, Brazil
| | - L M Teixeira
- Instituto de Microbiologia Paulo De Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro-RJ, Brazil
| | - P Marinho
- Maternidade Escola da Universidade Federal Do Rio Janeiro, Rio De Janeiro-RJ, Brazil
| | - S Taylor
- UK Health Security Agency, London, UK
| | - S Thomas
- UK Health Security Agency, London, UK
| | - T C A Pinto
- Instituto de Microbiologia Paulo De Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro-RJ, Brazil
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Røken M, Iakhno S, Haaland AH, Bjelland AM, Wasteson Y. The Home Environment Is a Reservoir for Methicillin-Resistant Coagulase-Negative Staphylococci and Mammaliicocci. Antibiotics (Basel) 2024; 13:279. [PMID: 38534714 DOI: 10.3390/antibiotics13030279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Coagulase-negative staphylococci (CoNS) and mammaliicocci are opportunistic human and animal pathogens, often resistant to multiple antimicrobials, including methicillin. Methicillin-resistant CoNS (MRCoNS) have traditionally been linked to hospitals and healthcare facilities, where they are significant contributors to nosocomial infections. However, screenings of non-hospital environments have linked MRCoNS and methicillin-resistant mammaliicocci (MRM) to other ecological niches. The aim of this study was to explore the home environment as a reservoir for MRCoNS and MRM. A total of 33 households, including households with a dog with a methicillin-resistant staphylococcal infection, households with healthy dogs or cats and households without pets, were screened for MRCoNS and MRM by sampling one human, one pet (if present) and the environment. Samples were analyzed by a selective culture-based method, and bacterial species were identified by MALDI-TOF MS and tested for antibiotic susceptibility by the agar disk diffusion method. Following whole-genome sequencing, a large diversity of SCCmec elements and sequence types was revealed, which did not indicate any clonal dissemination of specific strains. Virulome and mobilome analyses indicated a high degree of species specificity. Altogether, this study documents that the home environment is a reservoir for a variety of MRCoNS and MRM regardless of the type of household.
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Affiliation(s)
- Mari Røken
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
- Institute of Microbiology, Norwegian Armed Forces Joint Medical Services, 2027 Kjeller, Norway
| | | | - Anita Haug Haaland
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
- Regulations and Control Department, Animal Health, 0304 Oslo, Norway
| | - Ane Mohn Bjelland
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
- Department of Bacteriology, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | - Yngvild Wasteson
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
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Amer MA, Darwish MM, Soliman NS, Amin HM. Resistome, mobilome, and virulome explored in clinical isolates derived from acne patients in Egypt: unveiling unique traits of an emerging coagulase-negative Staphylococcus pathogen. Front Cell Infect Microbiol 2024; 14:1328390. [PMID: 38371297 PMCID: PMC10869526 DOI: 10.3389/fcimb.2024.1328390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/10/2024] [Indexed: 02/20/2024] Open
Abstract
Coagulase-negative staphylococci (CoNS) are a group of gram-positive staphylococcal species that naturally inhabit the healthy human skin and mucosa. The clinical impact of CoNS-associated infections has recently been regarded as a challenge for diagnosis and therapeutic options. CoNS-associated infections are primarily caused by bacterial resistance to antibiotics and biofilm formation. As antibiotics are still the most used treatment, this problem will likely persist in the future. The present study aimed to investigate the resistance and virulence of CoNS recovered from various acne lesions and explore their genetic basis. Skin swab samples were collected from participants with acne and healthy skin. All samples underwent conventional culture for the isolation of CoNS, MALDI-TOF confirmation, antibiotic susceptibility, and biofilm formation testing. A total of 85 CoNS isolates were recovered from the samples and preliminarily identified as Staphylococcus epidermidis. Isolates from the acne group (n = 60) showed the highest rates of resistance to penicillin (73%), cefoxitin (63%), clindamycin (53.3%), and erythromycin (48%), followed by levofloxacin (36.7%) and gentamycin (31.7%). The lowest rates of resistance were observed against tetracycline (28.3%), doxycycline (11.7%), and minocycline (8.3%). CoNS isolated from mild, moderate acne and healthy isolates did not show strong biofilm formation, whereas the isolates from the severe cases of the acne group showed strong biofilm formation (76.6%). Four extensively drug-resistant and strong biofilm-forming staphylococcal isolates recovered from patients with severe acne were selected for whole-genome sequencing (WGS), and their genomes were investigated using bioinformatics tools. Three of the sequenced genomes were identified as S. epidermidis; however, isolate 29AM was identified as Staphylococcus warneri, which is a newly emerging pathogen that is not commonly associated with acne and was not detected by MALDI-TOF. All the sequenced strains were multidrug-resistant and carried multiple resistance genes, including blaZ, mecA, tet(K), erm(C), lnuA, vgaA, dfrC, fusB, fosBx1, norA, and vanT, which were found to be located on plasmids and chromosomes. Virulence features were detected in all genomes in the presence of genes involved in adherence and biofilm formation (icaA, icaB, icaC, sdrG, sdrH, atl, ebh, and ebp). Only the S. warneri isolate 29AM contained immune evasion genes (capB, capC, acpXL, and manA), an anti-phagocytosis gene (cdsA), and other unique features. As a result of their potential pathogenicity and antibiotic resistance, CoNS must be monitored as an emerging pathogen associated with acne infections. To the best of our knowledge, this is the first report to isolate, identify, and correlate S. warneri with severe acne infections among Egyptian patients using WGS and bioinformatic analysis.
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Affiliation(s)
- Mai A. Amer
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts, Giza, Egypt
| | - Manal M. Darwish
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts, Giza, Egypt
- Medical Microbiology and Immunology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Noha S. Soliman
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Heba M. Amin
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts, Giza, Egypt
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Romero LC, Silva LP, Teixeira NB, de Camargo KV, Del Masso Pereira MA, Corrente JE, Pereira VC, Ribeiro de Souza da Cunha MDL. Staphylococcus capitis Bloodstream Isolates: Investigation of Clonal Relationship, Resistance Profile, Virulence and Biofilm Formation. Antibiotics (Basel) 2024; 13:147. [PMID: 38391533 PMCID: PMC10885910 DOI: 10.3390/antibiotics13020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Staphylococcus capitis has been recognized as a relevant opportunistic pathogen, particularly its persistence in neonatal ICUs around the world. Therefore, the aim of this study was to describe the epidemiological profile of clinical isolates of S. capitis and to characterize the factors involved in the persistence and pathogenesis of these strains isolated from blood cultures collected in a hospital in the interior of the state of São Paulo, Brazil. A total of 141 S. capitis strains were submitted to detection of the mecA gene and SCCmec typing by multiplex PCR. Genes involved in biofilm production and genes encoding enterotoxins and hemolysins were detected by conventional PCR. Biofilm formation was evaluated by the polystyrene plate adherence test and phenotypic resistance was investigated by the disk diffusion method. Finally, pulsed-field gel electrophoresis (PFGE) was used to analyze the clonal relationship between isolates. The mecA gene was detected in 99 (70.2%) isolates, with this percentage reaching 100% in the neonatal ICU. SCCmec type III was the most prevalent type, detected in 31 (31.3%) isolates and co-occurrence of SCCmec was also observed. In vitro biofilm formation was detected in 46 (32.6%) isolates but was not correlated with the presence of the ica operon genes. Furthermore, biofilm production in ICU isolates was favored by hyperosmotic conditions, which are common in ICUs because of the frequent parenteral nutrition. Analysis of the clonal relationship between the isolates investigated in the present study confirms a homogeneous profile of S. capitis and the persistence of clones that are prevalent in the neonatal ICU and disseminated across the hospital. This study highlights the adaptation of isolates to specific hospital environments and their high clonality.
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Affiliation(s)
- Letícia Calixto Romero
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-691, Brazil
| | - Lucas Porangaba Silva
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-691, Brazil
| | - Nathalia Bibiana Teixeira
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-691, Brazil
| | - Karen Vilegas de Camargo
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-691, Brazil
| | | | - José Eduardo Corrente
- Department of Biostatistics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-900, Brazil
| | - Valéria Cataneli Pereira
- Microbiology Laboratory, Universidade do Oeste Paulista (UNOESTE), Presidente Prudente 18618-970, Brazil
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Narongpun P, Chanchaithong P, Yamagishi J, Thapa J, Nakajima C, Suzuki Y. Whole-Genome Investigation of Zoonotic Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complex 398 Isolated from Pigs and Humans in Thailand. Antibiotics (Basel) 2023; 12:1745. [PMID: 38136779 PMCID: PMC10741195 DOI: 10.3390/antibiotics12121745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has been widespread globally in pigs and humans for decades. Nasal colonization of LA-MRSA is regarded as an occupational hazard to people who are regularly involved in livestock production. Our previous study suggested pig-to-human transmission caused by LA-MRSA clonal complex (CC) 398, using traditional molecular typing methods. Instead, this study aimed to investigate the zoonotic transmission of LA-MRSA CC398 using whole genome sequencing (WGS) technologies. A total of 63 LA-MRSA isolates were identified and characterized in Thailand. Further, the 16 representatives of LA-MRSA CC9 and CC398, including porcine and worker isolates, were subjected to WGS on the Illumina Miseq platform. Core-genome single nucleotide polymorphism (SNP)-based analyses verify the zoonotic transmission caused by LA-MRSA CC398 in two farms. WGS-based characterization suggests the emergence of a novel staphylococcal cassette chromosome (SCC) mec type, consisting of multiple cassette chromosome recombinase (ccr) gene complexes via genetic recombination. Additionally, the WGS analyses revealed putative multi-resistant plasmids and several cross-resistance genes, conferring resistance against drugs of last resort used in humans such as quinupristin/dalfopristin and linezolid. Significantly, LA-MRSA isolates, in this study, harbored multiple virulence genes that may become a serious threat to an immunosuppressive population, particularly for persons who are in close contact with LA-MRSA carriers.
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Affiliation(s)
- Pawarut Narongpun
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan; (P.N.)
| | - Pattrarat Chanchaithong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Junya Yamagishi
- Division of Collaboration and Education, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan; (P.N.)
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan; (P.N.)
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan; (P.N.)
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo 001-0020, Japan
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Wolska-Gębarzewska M, Międzobrodzki J, Kosecka-Strojek M. Current types of staphylococcal cassette chromosome mec (SCC mec) in clinically relevant coagulase-negative staphylococcal (CoNS) species. Crit Rev Microbiol 2023:1-17. [PMID: 37882662 DOI: 10.1080/1040841x.2023.2274841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
Coagulase-negative staphylococci (CoNS) colonize human skin and mucosal membranes, which is why they are considered harmless commensal bacteria. Two species, Staphylococcus epidermidis and Staphylococcus haemolyticus belong to the group of CoNS species and are most frequently isolated from nosocomial infections, including device-associated healthcare-associated infections (DA-HAIs) and local or systemic body-related infections (FBRIs). Methicillin resistance, initially described in Staphylococcus aureus, has also been reported in CoNS species. It is mediated by the mecA gene within the staphylococcal cassette chromosome (SCCmec). SCCmec typing, primarily using PCR-based methods, has been employed as a molecular epidemiological tool. However, the introduction of whole genome sequencing (WGS) and next-generation sequencing (NGS) has enabled the identification and verification of new SCCmec types. This review describes the current distribution of SCCmec types, subtypes, and variants among CoNS species, including S. epidermidis, S. haemolyticus, and S. capitis. The literature review focuses on recent research articles from the past decade that discuss new combinations of SCCmec in coagulase-negative Staphylococcus. The high genetic diversity and gaps in CoNS SCCmec annotation rules underscore the need for an efficient typing system. Typing SCCmec cassettes in CoNS strains is crucial to continuously updating databases and developing a unified classification system.
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Affiliation(s)
- Mariola Wolska-Gębarzewska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Jacek Międzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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Zhou J, Yang C, Lei W, Xu M, Cai X, Yuan W, Lin H. Identification and characterization of SCCmec typing with psm-mec positivity in staphylococci from patients with coagulase-negative staphylococci peritoneal dialysis-related peritonitis. BMC Microbiol 2023; 23:267. [PMID: 37742008 PMCID: PMC10517493 DOI: 10.1186/s12866-023-03017-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND Peritonitis is the most important complication of peritoneal dialysis (PD) and coagulase-negative staphylococci (CNS) are a frequent cause of dialysis-related infections. The association between SCCmec typing with psm-mec positivity in staphylococci and PD-related infections has not been identified. We aim to investigate the molecular epidemiology of CNS isolated from PD-peritonitis in a single Chinese center, focusing on the genetic determinants conferring methicillin resistance. METHODS We collected 10 genetically unrelated CNS isolates from 10 patients with CNS PD-related peritonitis. The patients were divided into two groups based on the results of MIC to oxacillin: the methicillin-resistant CNS (MRCNS) and methicillin-sensitive CNS (MSCNS) groups. The biofilm formation group (BFG) and the non-biofilm formation group (NBFG) were used as the control groups. Phenotypic and molecular methods were used to analyze SCCmec types I, II and III, associated genes and biofilm formation and the existence of psm-mec. The demographic data and clinical indicators were collected. RESULTS Ten CNS PD-related peritonitis patients were enrolled for this study. There were 6 MRCNS and 4 MRCNS isolates. SCCmec types were fully determined in 10 isolates. Seven staphylococci (70%) carried SCCmec, of which 4 isolates carried single SCCmec type I (40%) and 3 isolates had multiple SCCmec elements (I + III). Of the 6 MRCNS isolates, 3 carried SCCmec type I (50%) and 2 isolates carried SCCmec type I + III (33.3%). A high diversity of ccr types, mec complexes and ccr-mec complex combinations was identified among the 10 CNS isolates. The psm-mec gene was detected in 2/10 (20%) CNS isolates. There was no mutation in the psm-mec gene. CONCLUSIONS The majority of isolates were hospital-associated isolates. Furthermore, 2 psm-mec positive isolates were MRCNS in the NBFG. The PD patients frequent exposure to hospital would be the main risk factor. The presence of the psm-mec signal in the spectra of the MRCNS tested here demonstrates the presence of certain SCCmec cassettes that convey methicillin resistance.
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Affiliation(s)
- Jun Zhou
- Department of Nephrology and Rheumatology, Haikou People's Hospital Affiliated to Xiangya School of Medicine, Haikou, China
| | - Chuishun Yang
- Department of Nephrology and Rheumatology, Haikou People's Hospital Affiliated to Xiangya School of Medicine, Haikou, China
| | - Wenjuan Lei
- Department of Nephrology and Rheumatology, Haikou People's Hospital Affiliated to Xiangya School of Medicine, Haikou, China
| | - Man Xu
- Department of Nephrology and Rheumatology, Haikou People's Hospital Affiliated to Xiangya School of Medicine, Haikou, China
| | - Xingli Cai
- Department of Nephrology and Rheumatology, Haikou People's Hospital Affiliated to Xiangya School of Medicine, Haikou, China
| | - Wanqiong Yuan
- Department of Orthopedics, Peking University Third Hospital, No. 49 North Garden Road, Haidian District, Beijing, China.
- Beijing Key Laboratory of Spinal Disease, Beijing, China.
- Engineering Research Center of Bone and Joint Precision Medicine, Beijing, China.
| | - Hua Lin
- Department of Nursing, Haikou People's Hospital Affiliated to Xiangya School of Medicine, 43 Renmin Road, Haidian Island, Haikou, China.
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Zhou W, Jin Y, Shen P, Chen W, Chen Y, Xiao Y. Novel SCCmec variants in clonal complex 398 and lineage-specific pseudo-SCCmec identified in ST88 MRSA from invasive bloodstream infections in China. J Antimicrob Chemother 2023; 78:2366-2375. [PMID: 37552647 DOI: 10.1093/jac/dkad250] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Methicillin resistance in Staphylococcus aureus is primarily due to the mecA gene found in highly diverse staphylococcal cassette chromosome mec (SCCmec) elements, with an increasing number of variants being continually discovered. OBJECTIVES To characterize two novel SCCmec variants identified in clonal complex (CC) 398 strains and lineage-specific pseudo-SCCmec elements in the ST88 clone. METHODS WGS and comparative genomic analysis were used to elucidate the SCCmec element diversity of representative isolates. RESULTS The non-typeable 47 kb SCCmec found in the CC398 strain SKLX55795 represents a novel subtype of XIV, showing significant differences in structural organization and genetic content within the joining regions compared with the XIV element from the prototype strain SC792. This unique subtype comprised remnants from various mobile genetic elements that encode antimicrobial resistance genes, ultimately forming a large MDR region. Genome analysis of CC398 strain SKLX61416 revealed the presence of a novel 50 kb composite SCCmec with two distinct domains, carrying the ccr gene complexes 5/8 and containing genes for the detoxification of arsenic and sulphide. Further sequence analysis disclosed that 44.23% (23/52) of ST88 strains in our collection carried a lineage-specific pseudo-SCCmec, termed ΨSCCmecST88. This ΨSCCmecST88 harboured the mec gene complex C2, along with a series of genes associated with heavy metal resistance, but lacked an approximately 28 kb region encompassing the ccr gene complex. CONCLUSIONS Our findings provide evidence for the ongoing evolution of SCCmec elements within the CC398 and ST88 clones, underscoring the need for further surveillance to understand the biological significance of these elements.
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Affiliation(s)
- Wangxiao Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ye Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of General Intensive Care Unit, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Weiwei Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
- Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, China
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Phumthanakorn N, Wongsurawat T, Jenjaroenpun P, Kurilung A, Prapasarakul N. Novel Organization of the Staphylococcal Cassette Chromosome mec Composite Island in Clinical Staphylococcus haemolyticus and Staphylococcus hominis Subspecies hominis Isolates from Dogs. Microbiol Spectr 2022; 10:e0099722. [PMID: 35862947 PMCID: PMC9430635 DOI: 10.1128/spectrum.00997-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/16/2022] [Indexed: 11/23/2022] Open
Abstract
Staphylococcus haemolyticus and Staphylococcus hominis subsp. hominis are common coagulase-negative staphylococcus opportunistic pathogens. In Thailand, the clinical strains S. haemolyticus 1864 and 48 and S. hominis subsp. hominis 384 and 371 have been recovered from sick dogs. These strains were methicillin resistant with the nontypeable staphylococcal cassette chromosome mec (NT-SCCmec). The SCCmec element distribution in the clinical isolates from dogs was analyzed using whole-genome sequencing, which revealed the presence of different SCCmec composite islands (CIs) and gene structure. The SCCmec-CIs of ψSCCmec1864 (13 kb) and ψSCC1864 (11 kb) with a class C1 mec complex but no ccr gene were discovered in S. haemolyticus 1864. The CIs of ψSCCmec48 with a C1 mec complex (28 kb), SCC48 with ccrA4B4 (23 kb), and ψSCC48 (2.6 kb) were discovered in S. haemolyticus 48. In SCC48, insertion sequence IS256 contained an aminoglycoside-resistant gene [aph(2″)-Ia]. Two copies of IS431 containing the tetracycline-resistant gene tet(K) were found downstream of ψSCC48. In S. hominis subsp. hominis, the SCCmec-CI in strain 384 had two separate sections: ψSCCmec384 (20 kb) and SCCars (23 kb). ψSCCmec384 lacked the ccr gene complex but carried the class A mec complex. Trimethoprim-resistant dihydrofolate reductase (dfrC) was discovered on ψSCCmec384 between two copies of IS257. In strain 371, SCCmec VIII (4A) (37 kb) lacking a direct repeat at the chromosomal end was identified. This study found SCCmec elements in clinical isolates from dogs that were structurally complex and varied in their genetic content, with novel organization. IMPORTANCE In Thailand, the staphylococcal cassette chromosome mec (SCCmec) element, which causes methicillin resistance through acquisition of the mec gene, has been studied in clinical coagulase-negative Staphylococcus isolates from various companion animals, and Staphylococcus haemolyticus and Staphylococcus hominis subsp. hominis were found to have the most nontypeable (NT)-SCCmec elements. These species are more prone to causing illness and more resistant to a variety of antimicrobials than other coagulase-negative staphylococci. However, full characterization of NT-SCCmec in clinical S. haemolyticus and S. hominis subsp. hominis isolates from such animals has been limited. Our findings support the use of full nucleotide sequencing rather than PCR designed for Staphylococcus aureus in further research of novel SCCmec elements. Moreover, several antimicrobial resistance and heavy metal resistance genes were identified on the SCCmec elements; these are important as they could limit the therapeutic options available in veterinary medicine.
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Affiliation(s)
- Nathita Phumthanakorn
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
- Center of Excellence in Diagnostic and Monitoring of Animal Pathogens, Chulalongkorn University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Alongkorn Kurilung
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nuvee Prapasarakul
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Diagnostic and Monitoring of Animal Pathogens, Chulalongkorn University, Bangkok, Thailand
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El-Deeb W, Cave R, Fayez M, Alhumam N, Quadri S, Mkrtchyan HV. Methicillin Resistant Staphylococci Isolated from Goats and Their Farm Environments in Saudi Arabia Genotypically Linked to Known Human Clinical Isolates: a Pilot Study. Microbiol Spectr 2022; 10:e0038722. [PMID: 35913203 PMCID: PMC9431424 DOI: 10.1128/spectrum.00387-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/09/2022] [Indexed: 11/20/2022] Open
Abstract
We conducted a pilot whole genome sequencing (WGS) study to characterize the genotypes of nine methicillin resistant staphylococci (MRS) isolates recovered from goats and their farm environments in Eastern Province, Saudi Arabia, between November 2019 to August 2020. Seven out of nine isolates were methicillin resistant Staphylococcus aureus (MRSA), and two were methicillin resistant Staphylococcus epidermidis (MRSE). All MRSA isolates possessed genotypes previously identified to infect humans, including isolates harboring ST6-SCCmec IV-t304 (n = 4), ST5-SCCmec VI- t688 (n = 2) and ST5-SCCmec V-t311 (n = 1). 2 MRSA isolates possessed plasmids that were genetically similar to those identified in S. aureus isolates recovered from humans and poultry. In contrast, plasmids found in three MRSA isolates and one MRSE isolate were genetically similar to those recovered from humans. All MRSA isolates harbored the host innate modulate genes sak and scn previously associated with human infections. The genotypes of MRSE isolates were determined as ST35, a well-known zoonotic sequence type and ST153, which has been associated with humans. However, the MRSE isolates were untypeable due to extra ccr complexes identified in their SCCmec elements. Moreover, we identified in ST153 isolate SCCmec element also harbored the Arginine Catabolic Mobile Element (ACME) IV. All MRS isolates were phenotypically resistant to trimethoprim-sulfamethoxazole, an antibiotic for the decolonization of MRS. Three isolates carried antibiotic resistance genes in their SCCmec elements that were not previously described, including those encoding fusidic acid resistance (fusC) and trimethoprim resistance (dfrC) incorporated in the MRSA SCCmec VI. IMPORTANCE Our findings demonstrate a possible cross-transmission of methicillin resistant staphylococci between goats and their local environments and between goats and humans. Due to ever increasing resistance to multiple antibiotics, the burden of MRS has a significant impact on livestock farming, public health, and the economy worldwide. This study highlights that implementing a holistic approach to whole genome sequencing surveillance in livestock and farm environments would aid our understanding of the transmission of methicillin resistant staphylococci and, most importantly, allow us to implement appropriate infection control and hygiene practices.
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Affiliation(s)
- Wael El-Deeb
- Department of Clinical Sciences, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Al-Ahsa, Saudi Arabia
- Department of Internal Medicine, Infectious Diseases and Fish Diseases, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Rory Cave
- School of Biomedical Sciences, University of West London, London, United Kingdom
| | - Mahmoud Fayez
- Al Ahsa Veterinary Diagnostic Laboratory, Ministry of Environment, Water and Agriculture, Al-Hofuf, Al-Ahsa, Saudi Arabia
- Veterinary Serum and Vaccine Research Institute, Ministry of Agriculture, Cairo, Egypt
| | - Naser Alhumam
- Department of Microbiology and parasitology, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Al-Ahsa, Saudi Arabia
| | - Sayed Quadri
- Division of Microbiology and Immunology, Department of Biomedical Sciences, College of Medicine, King Faisal University, Al-Hofuf, Al-Ahsa, Kingdom of Saudi Arabia
| | - Hermine V. Mkrtchyan
- School of Biomedical Sciences, University of West London, London, United Kingdom
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Calefi DG, Haddad JPA, Pedroso SHSP, Magalhães PP, Farias LM, Vieira CD, Dos Santos SG. Evidence of cross-contamination of waste workers and transmission of antimicrobial resistance genes by coagulase-negative Staphylococcus isolated from dental solid waste: an intriguing study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:1291-1303. [PMID: 33499654 DOI: 10.1080/09603123.2021.1877634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
The aim of this study was to phenotypically and genotypically identify coagulase-negative Staphylococcus (CoNS) recovered from the nostrils of waste workers and from dental waste; 135 strains were recovered and S. epidermidis was the prevailing species. Genetic similarity (100%) was observed between the two S. epidermidis isolated from different employees on the same shift and 85% similarity between the S. epidermidis recovered from an employee's nostril and from waste. The mecA gene was found in 20 CoNS, and 20% were also found to possess the vanA gene. The blaZ gene was detected in 46.7%, and the icaA (34.8%), B and C genes (11.8% each). Our findings emphasized the biological risk to which waste workers are exposed and unprecedently confirms that it was possible to recover genetically identical bacterial species from waste and from workers' nostrils. It is important to highlight that this risk is raised by the detection of relevant antimicrobial resistance genes. The results also suggest that effective measures to correctly manage waste and promote the rational use of antimicrobials should be adopted.
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Affiliation(s)
- Débora Guimarães Calefi
- Departamento De Microbiologia, Instituto De Ciências Biológicas, Universidade Federal De Minas Gerais, Belo Horizonte, Brasil
| | - João Paulo Amaral Haddad
- Departamento De Medicina Veterinária Preventiva, Faculdade De Veterinária, Universidade Federal De Minas Gerais, Belo Horizonte, Brasil
| | | | - Paula Prazeres Magalhães
- Departamento De Microbiologia, Instituto De Ciências Biológicas, Universidade Federal De Minas Gerais, Belo Horizonte, Brasil
| | - Luiz Macêdo Farias
- Departamento De Microbiologia, Instituto De Ciências Biológicas, Universidade Federal De Minas Gerais, Belo Horizonte, Brasil
| | - Cristina Dutra Vieira
- Departamento De Microbiologia, Instituto De Ciências Biológicas, Universidade Federal De Minas Gerais, Belo Horizonte, Brasil
| | - Simone Gonçalves Dos Santos
- Departamento De Microbiologia, Instituto De Ciências Biológicas, Universidade Federal De Minas Gerais, Belo Horizonte, Brasil
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Ho PL, Law YH, Liu MCJ, Lau A, Tong MK, Chow KH, Wu AKL, Tse CWS, Cheng VCC, Que TL. Improved Detection of mecA-Mediated β-Lactam Resistance in Staphylococcus lugdunensis Using a New Oxacillin Salt Agar Screen. Front Microbiol 2021; 12:704552. [PMID: 34421864 PMCID: PMC8378274 DOI: 10.3389/fmicb.2021.704552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/14/2021] [Indexed: 11/14/2022] Open
Abstract
Oxacillin resistance mediated by mecA in Staphylococcus lugdunensis is emerging in some geographic areas. We evaluated cefoxitin disk diffusion (DD) and a new oxacillin agar (supplemented with 2 μg/ml oxacillin and 2% sodium chloride) screen for the detection of mecA-mediated resistance in S. lugdunensis. A total of 300 consecutive, non-duplicated clinical S. lugdunensis isolates from diverse sources in Hong Kong in 2019 were tested. The categorical agreement and errors obtained between cefoxitin DD test, oxacillin agar screen and mecA PCR were analyzed. Isolates with discordant results were further tested by MIC, penicillin binding protein 2a (PBP2a) assays, population analysis and molecular typing. PCR showed that 62 isolates were mecA-positive and 238 isolates were mecA-negative. For cefoxitin DD results interpreted using S. aureus/S. lugdunensis breakpoints, the categorical agreement (CA) for two brands of Muller-Hinton agars, MH-II (Becton Dickinson) and MH-E (bioMérieux) were both 96.0%; MEs were both 0%; and VMEs were 19.4 and 12.9%, respectively. The new oxacillin agar reliably differentiated mecA-positive and mecA-negative isolates (100% CA) without any ME or VME results. The 8 isolates with false susceptibility in the cefoxitin DD testing had cefoxitin and oxacillin MICs in the susceptible range. The isolates showed heterogeneous oxacillin resistance with resistant subpopulations at low frequencies. All had positive PBP2a results and were typed as sequence type 27/SCCmec V. The findings highlight the inability of cefoxitin DD and MIC tests for reliable detection of some mecA-positive S. lugdunensis isolates.
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Affiliation(s)
- Pak-Leung Ho
- Department of Microbiology, Queen Mary Hospital, University of Hong Kong, Hong Kong, China.,Carol Yu Center for Infection, University of Hong Kong, Hong Kong, China
| | - Ying-Hang Law
- Department of Clinical Pathology, Tuen Mun Hospital, Hospital Authority, Hong Kong, China
| | - Melissa Chun-Jiao Liu
- Department of Microbiology, Queen Mary Hospital, University of Hong Kong, Hong Kong, China
| | - Andes Lau
- Department of Microbiology, Queen Mary Hospital, University of Hong Kong, Hong Kong, China
| | - Man-Ki Tong
- Department of Microbiology, Queen Mary Hospital, University of Hong Kong, Hong Kong, China
| | - Kin-Hung Chow
- Department of Microbiology, Queen Mary Hospital, University of Hong Kong, Hong Kong, China
| | - Alan Ka-Lun Wu
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hospital Authority, Hong Kong, China
| | - Cindy Wing-Sze Tse
- Department of Clinical Pathology, Kwong Wah Hospital, Hospital Authority, Hong Kong, China
| | | | - Tak-Lun Que
- Department of Clinical Pathology, Tuen Mun Hospital, Hospital Authority, Hong Kong, China
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Characterizing a novel SCC mec with a composite structure from a clinical strain of Staphylococcus hominis, C34847. Antimicrob Agents Chemother 2021; 65:e0077721. [PMID: 34370581 DOI: 10.1128/aac.00777-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcal cassette chromosome mec (SCCmec) has predominantly been described in methicillin-resistant Staphylococcus aureus. However, studies have indicated that coagulase-negative staphylococci (CoNS) carry a larger diversity of SCC elements. We characterized a composite SCCmec element carrying an uncharacterized ccr1 and type A mec gene combination, in conjunction with a secondary element bearing ccr4, from a clinical strain of S. hominis. The element's complex structure points to a high degree of recombination occurring in SCCmec in CoNS.
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Lienen T, Schnitt A, Hammerl JA, Marino SF, Maurischat S, Tenhagen BA. Multidrug-resistant Staphylococcus cohnii and Staphylococcus urealyticus isolates from German dairy farms exhibit resistance to beta-lactam antibiotics and divergent penicillin-binding proteins. Sci Rep 2021; 11:6075. [PMID: 33727647 PMCID: PMC7966787 DOI: 10.1038/s41598-021-85461-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/24/2021] [Indexed: 11/09/2022] Open
Abstract
Non-aureus staphylococci are commonly found on dairy farms. Two rarely investigated species are Staphylococcus (S.) cohnii and S. urealyticus. Since multidrug-resistant S. cohnii and S. urealyticus are known, they may serve as an antimicrobial resistance (AMR) gene reservoir for harmful staphylococcal species. In our study, nine S. cohnii and six S. urealyticus isolates from German dairy farms were analyzed by whole-genome sequencing and AMR testing. The isolates harbored various AMR genes (aadD1, str, mecA, dfrC/K, tetK/L, ermC, lnuA, fexA, fusF, fosB6, qacG/H) and exhibited non-wildtype phenotypes (resistances) against chloramphenicol, clindamycin, erythromycin, fusidic acid, rifampicin, streptomycin, tetracycline, tiamulin and trimethoprim. Although 14/15 isolates lacked the blaZ, mecA and mecC genes, they showed reduced susceptibility to a number of beta-lactam antibiotics including cefoxitin (MIC 4-8 mg/L) and penicillin (MIC 0.25-0.5 mg/L). The specificity of cefoxitin susceptibility testing for mecA or mecC gene prediction in S. cohnii and S. urealyticus seems to be low. A comparison with penicillin-binding protein (PBP) amino acid sequences of S. aureus showed identities of only 70-80% with regard to PBP1, PBP2 and PBP3. In conclusion, S. cohnii and S. urealyticus from selected German dairy farms show multiple resistances to antimicrobial substances and may carry unknown antimicrobial resistance determinants.
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Affiliation(s)
- Tobias Lienen
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany.
| | - Arne Schnitt
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany
| | - Jens Andre Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany
| | - Stephen F Marino
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany
| | - Sven Maurischat
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany
| | - Bernd-Alois Tenhagen
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany.
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15
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Cole K, Atkins B, Llewelyn M, Paul J. Genomic investigation of clinically significant coagulase-negative staphylococci. J Med Microbiol 2021; 70. [PMID: 33704043 DOI: 10.1099/jmm.0.001337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Introduction. Coagulase-negative staphylococci have been recognized both as emerging pathogens and contaminants of clinical samples. High-resolution genomic investigation may provide insights into their clinical significance.Aims. To review the literature regarding coagulase-negative staphylococcal infection and the utility of genomic methods to aid diagnosis and management, and to identify promising areas for future research.Methodology. We searched Google Scholar with the terms (Staphylococcus) AND (sequencing OR (infection)). We prioritized papers that addressed coagulase-negative staphylococci, genomic analysis, or infection.Results. A number of studies have investigated specimen-related, phenotypic and genetic factors associated with colonization, infection and virulence, but diagnosis remains problematic.Conclusion. Genomic investigation provides insights into the genetic diversity and natural history of colonization and infection. Such information allows the development of new methodologies to identify and compare relatedness and predict antimicrobial resistance. Future clinical studies that employ suitable sampling frames coupled with the application of high-resolution whole-genome sequencing may aid the development of more discriminatory diagnostic approaches to coagulase-staphylococcal infection.
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Affiliation(s)
- Kevin Cole
- Brighton and Sussex Medical School, Brighton, UK.,Public Health England Collaborating Centre, Royal Sussex County Hospital, Brighton, UK
| | | | - Martin Llewelyn
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK.,Brighton and Sussex Medical School, Brighton, UK
| | - John Paul
- Public Health England Collaborating Centre, Royal Sussex County Hospital, Brighton, UK.,Brighton and Sussex Medical School, Brighton, UK
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Shokravi Z, Haseli M, Mehrad L, Ramazani A. Distribution of Staphylococcal cassette chromosome mecA (SCCmec) types among coagulase-negative Staphylococci isolates from healthcare workers in the North-West of Iran. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2020; 23:1489-1493. [PMID: 33235707 PMCID: PMC7671417 DOI: 10.22038/ijbms.2020.48481.11127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Objectives Methicillin-resistant coagulase-negative Staphylococci (MR-CoNS) are recognized as one of the major causes of healthcare-associated infections in hospitals. The present investigation aimed to study the prevalence of Staphylococcal cassette chromosome mec (SCCmec) types, along with aminoglycoside modifying enzymes (AMEs) genes in the nasal carriage of MR-CoNS in the north-west of Iran. Materials and Methods To assess the potential of coagulase-negative Staphylococci as hidden reservoirs for antibiotic resistance, we analyzed the antimicrobial susceptibility of MR-CoNS using the disk diffusion method. In addition, PCR and multiplex PCR assays were performed to determine the prevalence of AME encoding genes and SCCmec types in methicillin-resistant coagulase-negative Staphylococci isolates. Results A total of 51 MR-CoNS isolates were recovered from the anterior nares of healthcare workers. The observed resistance rates to tobramycin, gentamicin, cotrimoxazole, kanamycin, erythromycin, tetracycline, and ciprofloxacin were 74.5%, 68.5%, 57%, 53%, 51%, 49%, and 8%, respectively. Of the 51 tested MR-CoNS isolates, 2(4%) were harboring SCCmec type I, four (8%) were type II, six (12%) type III, eleven (21.6%) type IVa, two (4%) type IVb, two (4%) type IVc, six (12%) type IVd, and two (4%) type V. The rates of prevalence of the aminoglycoside modifying enzyme genes were as follows: aac (6')/aph (2'') (28 cases, 55 %), ant (4')-Ia (20 cases, 39%), and the aph (3´)-IIIa gene (9 cases, 17.6 %). Conclusion Subtypes IVa and IVd were the most prevalent SCC elements, and aac (6')/aph (2'') was the most common AME gene detected among the MR-CoNS isolates.
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Affiliation(s)
- Zahra Shokravi
- Department of Microbiology, Faculty of Basic Science, Islamic Azad University, Science and Research Branch of Tehran, Markazi, Iran
| | - Mehdi Haseli
- Biotechnology Department, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Laleh Mehrad
- Department of Microbiology, Faculty of Basic Science, Islamic Azad University, Science and Research Branch of Tehran, Markazi, Iran
| | - Ali Ramazani
- Biotechnology Department, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
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Kumari H, Chakraborti T, Singh M, Chakrawarti MK, Mukhopadhyay K. Prevalence and antibiogram of coagulase negative Staphylococci in bioaerosols from different indoors of a university in India. BMC Microbiol 2020; 20:211. [PMID: 32677881 PMCID: PMC7364608 DOI: 10.1186/s12866-020-01875-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/25/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Staphylococci species are the major constituents of infectious bioaerosols, particularly methicillin-resistant Staphylococci (MRS) have serious health impacts. Here, the bacterial burden was quantified, especially prevalence of MRS in bioaerosols collected from indoors of Dr. B.R. Ambedkar Central Library (DBRACL) and Central Laboratory Animal Resources (CLAR) of Jawaharlal Nehru University, New Delhi, India. Air samplings from DBRACL and CLAR were done using the settle plate method and SKC biosampler, respectively. RESULTS This study showed a maximum 6757 CFU/m2/hr of bacterial load in the DBRACL reading room, while unacceptable bacterial loads (> 1000 CFU/m3 of air) at different sites of CLAR. Further, at both the sampling sites the predominance of coagulase negative Staphylococci (CNS) was observed. A total 22 and 35 Staphylococci isolates were isolated from DBRACL and CLAR bioaerosols, respectively. Majority (16/22) of the Staphylococcal isolates from DBRACL belonged to human-associated Staphylococci where S. haemolyticus (5/22) was the most dominating species. However, in CLAR facility centre, animal-associated Staphylococci (19/35) were dominating, where S. xylosus (12/35) was the most dominating species. Further, antibiotic sensitivity tests revealed 41% MRS and 73% multidrug resistant (MDR) among airborne Staphylococci from DBRACL indoor bioaerosols. Similarly, in CLAR facility, approximately, 66% Staphylococci isolates were methicillin resistant, out of which 2 isolates showed high MIC value ≥ 16 μg/mL. Further, we confirmed the presence of 49% multidrug resistant Staphylococci in the indoor air of CLAR facility. CONCLUSIONS This study suggested that the exposure of workers and students in CLAR to such a high concentration of drug-resistant Staphylococci should not be undermined, as these bacterial concentrations are the direct representative of inhalable particulate matter (PM2.5) as per collection procedure. Simultaneously, passive sampling from DBRACL assessed the risks due to microbial contamination in particle agglomerates, which may deposit on the crucial surfaces such as wounds/ cuts or on the frequently used items.
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Affiliation(s)
- Himani Kumari
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Trina Chakraborti
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Madhuri Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | | | - Kasturi Mukhopadhyay
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Kosecka-Strojek M, Sadowy E, Gawryszewska I, Klepacka J, Tomasik T, Michalik M, Hryniewicz W, Miedzobrodzki J. Emergence of linezolid-resistant Staphylococcus epidermidis in the tertiary children's hospital in Cracow, Poland. Eur J Clin Microbiol Infect Dis 2020; 39:1717-1725. [PMID: 32350737 PMCID: PMC7427702 DOI: 10.1007/s10096-020-03893-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 04/01/2020] [Indexed: 11/26/2022]
Abstract
Coagulase-negative staphylococci, ubiquitous commensals of human skin, and mucous membranes represent important pathogens for immunocompromised patients and neonates. The increasing antibiotic resistance among Staphylococcus epidermidis is an emerging problem worldwide. In particular, the linezolid-resistant S. epidermidis (LRSE) strains are observed in Europe since 2014. The aim of our study was to genetically characterize 11 LRSE isolates, recovered mostly from blood in the University Children’s Hospital in Krakow, Poland, between 2015 and 2017. For identification of the isolates at the species level, we used 16S rRNA sequencing and RFLP of the saoC gene. Isolates were characterized phenotypically by determining their antimicrobial resistance patterns and using molecular methods such as PFGE, MLST, SCCmec typing, detection of the ica operon, and analysis of antimicrobial resistance determinants. All isolates were multidrug-resistant, including resistance to methicillin, and exhibited so-called PhLOPSA phenotype. In PFGE, all isolates (excluding one from a catheter) represented identical patterns, were identified as ST2, and harbored the ica operon, responsible for biofilm formation. Linezolid resistance was associated with acquisition of A157R mutation in the ribosomal protein L3 and the presence of cfr gene. All isolates revealed new SCCmec cassette element composition. Recently, pediatric patients with serious staphylococcal infections are often treated with linezolid. The increasing linezolid resistance in bacterial strains becomes a real threat for patients, and monitoring such infections combined with surveillance and infection prevention programs is very important to decrease number of linezolid-resistant staphylococcal strains.
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Affiliation(s)
- Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Iwona Gawryszewska
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Joanna Klepacka
- Department of Clinical Microbiology, Children's University Hospital, Jagiellonian University, Krakow, Poland
| | - Tomasz Tomasik
- Department of Clinical Microbiology, Children's University Hospital, Jagiellonian University, Krakow, Poland
| | | | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Jacek Miedzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.
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Cave R, Misra R, Chen J, Wang S, Mkrtchyan HV. Whole genome sequencing revealed new molecular characteristics in multidrug resistant staphylococci recovered from high frequency touched surfaces in London. Sci Rep 2019; 9:9637. [PMID: 31371820 PMCID: PMC6675788 DOI: 10.1038/s41598-019-45886-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/13/2019] [Indexed: 01/15/2023] Open
Abstract
The rise of antibiotic resistance (AMR) is one of the most important public health threats worldwide.Today, increasing attention is being paid to multidrug resistant staphylococci isolated from healthcare and non-healthcare environments as the treatment of these bacteria has become increasingly difficult. In this study, we compared staphylococci isolates recovered from high frequency touched surfaces from public areas in the community and hospitals in East and West London. 281 out of 600 (46.83%) staphylococci isolates recovered were multidrug resistant, of which 49 (8.17%) were mecA positive. There was significantly higher proportion of multidrug resistant staphylococci (P = 0.0002) in East London (56.7%) compared to West London (49.96%). The most common species identified as multidrug resistant were S. epidermidis, S. haemolyticus and S. hominis, whereas penicillin, fusidic acid and erythromycin were the most frequent antibiotics the isolates were resistant to. Whole genome sequenced of mecA positive isolates revealed that S. sciuri isolates carried the mecA1 gene, which has only 84.43% homology with mecA. In addition, other frequently identified resistance genes included blaZ, qacA/B and dfrC. We have also identified a diverse range of SCCmec types, many of which were untypable due to carrying a novel combination of ccr genes or multiple ccr complexes.
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Affiliation(s)
- Rory Cave
- University of East London, School of Health, Sport and Bioscience, Water Lane, London, E15 4LZ, UK
| | - Raju Misra
- Natural History Museum, Core Research Laboratories, Molecular Biology, Cromwell Rd, London, SW7 5BD, UK
| | - Jiazhen Chen
- Department of Infectious Disease, Huashan Hospital, Fudan University, 12 Middle Wulumuqi Rd., Shanghai, 200040, China
| | - Shiyong Wang
- Department of Infectious Disease, Huashan Hospital, Fudan University, 12 Middle Wulumuqi Rd., Shanghai, 200040, China
| | - Hermine V Mkrtchyan
- University of East London, School of Health, Sport and Bioscience, Water Lane, London, E15 4LZ, UK.
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Bhowmik D, Chakraborty P, Bhowmick R, Sarkar R, Chetri S, Bhattacharjee A. Occurrence of II and V staphylococcal cassette chromosome mec types among coagulase-negative staphylococci from Northeastern part of India. Indian J Med Microbiol 2019; 36:522-525. [PMID: 30880700 DOI: 10.4103/ijmm.ijmm_18_285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Introduction Coagulase Negative Staphylococci, the most commonly isolated pathogen are becoming emerging threats to the community as well as to the nosocomial environment. The present study underscores the distribution of Staphylococcal cassette chromosome mec (SCCmec) types among Methicillin resistant Coagulase Negative Staphylococci from the environmental origin. Methods and Materials Environmental and food sample (n = 460) from different location of northeastern region of India were collected for a period of one year and were phenotypically and genotypically screened using cefoxitin disc and PCR techniques for mecA and mecC gene detection. All the MR-CoNS isolates possessing mecA gene were subjected to 16srDNA sequencing for species identification. SCCmec typing was determined by evaluating using primer sets from type I to type V. Antibiotic susceptibility testing was performed for all the isolates. Statistical analysis with chi-square test using SPSS-21 statistical software. Results Methicillin resistance shown by one hundred forty three isolates were carried out for molecular analysis, among them 53.84% serves as mecA carrier. Distribution of Staphylococcus haemolyticus was more frequent and was found that SCCmec types II and V were predominant among the study isolates. Linezolid was the drug of choice for the CoNS isolates. Statistical analysis showed an insignificant result for the tested antibiotics and SCCmec types. Conclusion This study therefore interprets the relative importance of SCCmec types among MR-CoNS isolates.
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Affiliation(s)
| | | | | | - Rakesh Sarkar
- Department of Microbiology, Assam University, Silchar, Assam, India
| | - Shiela Chetri
- Department of Microbiology, Assam University, Silchar, Assam, India
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Ekinci B, Edgunlu TG, Bayramoglu G, Atay GU. Molecular investigation of staphylococcal cassette chromosome mec types and genotypic relations of methicillin-resistant staphylococci isolated from before and after hospital exposed students. Indian J Med Microbiol 2018; 36:257-264. [PMID: 30084421 DOI: 10.4103/ijmm.ijmm_17_256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background Reservoir of methicillin resistance genes called staphylococcal cassette chromosome mec (SCCmec), plasmids and genomic characterisations of isolates have been widely investigated in epidemiologic research. However, the extent to which these organisms are transported by patients or hospital staff is not entirely clear. Aim This study aims to investigate the molecular relatedness and plasmid profiles of MR staphylococci isolated from nursing students before and after hospital training, to find out the possible source. Materials and Methods This study examined 39 methicillin-resistant (MR) staphylococci and 2 inducible clindamycin-resistant, methicillin-susceptible Staphylococcus aureus. Specimens were collected before and after 4 months of hospital training from the hands and nares of 75 nursing students. A polymerase chain reaction technique was used to confirm the existence of mecA gene and identify SCCmec types; total DNA was digested by SmaI endonuclease restriction to monitorise clonal relatedness by pulsed-field gel electrophoresis (PFGE); plasmid profiles were monitorised on agarose gel. Results All 39 isolates tested positive for mecA; SCCmec type III was observed most frequently. Interestingly, in one isolate of Staphylococcus epidermidis, four different types of SCCmec elements were observed. There were 23 different types of plasmids, whose sizes ranged from 1.4 to 46.0 kb. After PFGE dendogram analysis, two strains were classified as indistinguishable; six were closely related. Most of the isolates obtained after hospital training showed clonal similarity and seven had multiple SCCmec elements require further investigation for the possible mechanism. Conclusion Most of the isolates obtained after hospital training showed clonal similarity and seven had multiple SCCmec elements require further investigation for the possible mechanism.
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Affiliation(s)
- Bora Ekinci
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Mugla Sitki Kocman University, Mugla, Turkey
| | - Tuba Gokdogan Edgunlu
- Department of Medical Biology, Faculty of Medicine, Mugla Sitki Kocman University, Mugla, Turkey
| | - Gulcin Bayramoglu
- Department of Medical Microbiology, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Gulsen Ulucam Atay
- Department of Medical Microbiology, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
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