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Magnan C, Morsli M, Salipante F, Thiry B, Attar JE, Maio MD, Safaria M, Tran TA, Dunyach-Remy C, Ory J, Richaud-Morel B, Sotto A, Pantel A, Lavigne JP. Emergence of multidrug-resistant Staphylococcus haemolyticus in neonatal intensive care unit in Southern France, a genomic study. Emerg Microbes Infect 2024; 13:2353291. [PMID: 38738561 PMCID: PMC11132433 DOI: 10.1080/22221751.2024.2353291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 05/03/2024] [Indexed: 05/14/2024]
Abstract
An emergence of multidrug-resistant (MDR) Staphylococcus haemolyticus has been observed in the neonatal intensive care unit (NICU) of Nîmes University Hospital in southern France. A case-control analysis was conducted on 96 neonates, to identify risk factors associated with S. haemolyticus infection, focusing on clinical outcomes. Forty-eight MDR S. haemolyticus strains, isolated from neonates between October 2019 and July 2022, were investigated using routine in vitro procedures and whole-genome sequencing. Additionally, five S. haemolyticus isolates from adult patients were sequenced to identify clusters circulating within the hospital environment. The incidence of neonatal S. haemolyticus was significantly associated with low birth weight, lower gestational age, and central catheter use (p < 0.001). Sepsis was the most frequent clinical manifestation in this series (20/46, 43.5%) and was associated with five deaths. Based on whole-genome analysis, three S. haemolyticus genotypes were predicted: ST1 (6/53, 11%), ST25 (3/53, 5.7%), and ST29 (44/53, 83%), which included the subcluster II-A, predominantly emerging in the neonatal department. All strains were profiled in silico to be resistant to methicillin, erythromycin, aminoglycosides, and fluoroquinolones, consistent with in vitro antibiotic susceptibility tests. Moreover, in silico prediction of biofilm formation and virulence-encoding genes supported the association of ST29 with severe clinical outcomes, while the persistence in the NICU could be explained by the presence of antiseptic and heavy metal resistance-encoding genes. The clonality of S. haemolyticus ST29 subcluster II-A isolates confirms healthcare transmission causing severe infections. Based on these results, reinforced hygiene measures are necessary to eradicate the nosocomial transmission of MDR strains.
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Affiliation(s)
- Chloé Magnan
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Madjid Morsli
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Florian Salipante
- Department of Biostatistics, Epidemiology, Public Health and Innovation in Methodology, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Blandine Thiry
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Julie El Attar
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Massimo Di Maio
- Neonatal Pediatrics Department, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Maryam Safaria
- Neonatal Pediatrics Department, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Tu-Anh Tran
- Department of Paediatrics, CHU Nîmes, Nîmes, France
| | - Catherine Dunyach-Remy
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Jérôme Ory
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Brigitte Richaud-Morel
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Albert Sotto
- VBIC, Univ Montpellier, INSERM U1047, Department of Infectious Diseases, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Alix Pantel
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Jean-Philippe Lavigne
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
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Jesumirhewe C, Odufuye TO, Ariri JU, Adebiyi AA, Sanusi AT, Stöger A, Daza-Prieto B, Allerberger F, Cabal-Rosel A, Ruppitsch W. Genetic Characterization of Antibiotic-Resistant Staphylococcus spp. and Mammaliicoccus sciuri from Healthy Humans and Poultry in Nigeria. Antibiotics (Basel) 2024; 13:733. [PMID: 39200033 PMCID: PMC11350800 DOI: 10.3390/antibiotics13080733] [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: 06/14/2024] [Revised: 07/18/2024] [Accepted: 07/29/2024] [Indexed: 09/01/2024] Open
Abstract
Staphylococcus spp. poses a significant threat to human and animal health due to their capacity to cause a wide range of infections in both. In this study, resistance genes conferring antibiotic resistance in Staphylococcus spp. and Mammaliicoccus sciuri isolates from humans and poultry in Edo state, Nigeria, were investigated. In April 2017, 61 Staphylococcus spp. isolates were obtained from urine, wounds, nasal and chicken fecal samples. Species identification was carried out by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Antimicrobial susceptibility testing was performed using the Kirby-Bauer method for 16 antibiotics. Whole-genome sequencing was used for characterization of the isolates. The 61 investigated isolates included Staphylococcus aureus, S. arlettae, M. sciuri, S. haemolyticus, and S. epidermidis. A total of 47 isolates (77%) belonged to human samples and 14 (23%) isolates were collected from poultry samples. All were phenotypically resistant to at least three antimicrobial(s). Multiple resistance determinants were detected in the human and poultry isolates analyzed. Phylogenetic analysis revealed close relatedness among the isolates within each species for S. arlettae, M. sciuri, and S. haemolyticus, respectively. This study delivered comprehensive genomic insights into antibiotic-resistant Staphylococcus species and M. sciuri isolates from human and poultry sources in Edo state, Nigeria, from a One Health perspective.
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Affiliation(s)
- Christiana Jesumirhewe
- Department of Pharmaceutical Microbiology, College of Pharmacy, Igbinedion University Okada, Okada 302111, Edo State, Nigeria; (T.O.O.); (J.U.A.); (A.A.A.); (A.T.S.)
| | - Tolulope Oluwadamilola Odufuye
- Department of Pharmaceutical Microbiology, College of Pharmacy, Igbinedion University Okada, Okada 302111, Edo State, Nigeria; (T.O.O.); (J.U.A.); (A.A.A.); (A.T.S.)
| | - Juliana Ukinebo Ariri
- Department of Pharmaceutical Microbiology, College of Pharmacy, Igbinedion University Okada, Okada 302111, Edo State, Nigeria; (T.O.O.); (J.U.A.); (A.A.A.); (A.T.S.)
| | - Amdallat Arike Adebiyi
- Department of Pharmaceutical Microbiology, College of Pharmacy, Igbinedion University Okada, Okada 302111, Edo State, Nigeria; (T.O.O.); (J.U.A.); (A.A.A.); (A.T.S.)
| | - Amina Tanko Sanusi
- Department of Pharmaceutical Microbiology, College of Pharmacy, Igbinedion University Okada, Okada 302111, Edo State, Nigeria; (T.O.O.); (J.U.A.); (A.A.A.); (A.T.S.)
| | - Anna Stöger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.S.); (B.D.-P.); (F.A.); (A.C.-R.); (W.R.)
| | - Beatriz Daza-Prieto
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.S.); (B.D.-P.); (F.A.); (A.C.-R.); (W.R.)
| | - Franz Allerberger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.S.); (B.D.-P.); (F.A.); (A.C.-R.); (W.R.)
| | - Adriana Cabal-Rosel
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.S.); (B.D.-P.); (F.A.); (A.C.-R.); (W.R.)
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.S.); (B.D.-P.); (F.A.); (A.C.-R.); (W.R.)
- Faculty of Food Technology, Food Safety and Ecology, University of Donja Gorica, 81000 Podgorica, Montenegro
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Westberg R, Stegger M, Söderquist B. Molecular Epidemiology of Neonatal-Associated Staphylococcus haemolyticus Reveals Endemic Outbreak. Microbiol Spectr 2022; 10:e0245222. [PMID: 36314976 PMCID: PMC9769988 DOI: 10.1128/spectrum.02452-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
Staphylococcus haemolyticus is a major cause of late-onset sepsis in neonates, and endemic clones are often multidrug-resistant. The bacteria can also act as a genetic reservoir for more pathogenic bacteria. Molecular epidemiology is important in understanding bacterial pathogenicity and preventing infection. To describe the molecular epidemiology of S. haemolyticus isolated from neonatal blood cultures at a Swedish neonatal intensive care unit (NICU) over 4 decades, including antibiotic resistance genes (ARGs), virulence factors, and comparison to international isolates. Isolates were whole-genome sequenced, and single nucleotide polymorphisms in the core genome were used to map the relatedness. The occurrence of previously described ARGs and virulence genes were investigated. Disc diffusion and gradient tests were used to determine phenotypic resistance. The results revealed a clonal outbreak of S. haemolyticus at this NICU during the 1990s. Multidrug resistance was present in 28 (82%) of all isolates and concomitant resistance to aminoglycoside and methicillin occurred in 27 (79%). No isolates were vancomycin resistant. Genes encoding ARGs and virulence factors occurred frequently. The isolates in the outbreak were more homogenous in their genotypic and phenotypic patterns. Genotypic and phenotypic resistance combinations were consistent. Pathogenic traits previously described in S. haemolyticus occurred frequently in the present isolates, perhaps due to the hospital selection pressure resulting in epidemiological success. The clonal outbreak revealed by this study emphasizes the importance of adhering to hygiene procedures in order to prevent future endemic outbreaks. IMPORTANCE This study investigated the relatedness of Staphylococcus haemolyticus isolated from neonatal blood and revealed a clonal outbreak in the 1990s at a Swedish neonatal intensive care unit. The outbreak clone has earlier been isolated in Japan and Norway. Virulence and antibiotic resistance genes previously associated with clinical S. haemolyticus were frequently occuring in the present study as well. The majority of the isolates were multidrug-resistant. These traits should be considered important for S. haemolyticus epidemiological success and are probably caused by the hospital selection pressure. Thus, this study emphasizes the importance of restrictive antibiotic use and following the hygiene procedures, to prevent further antibiotic resistance spread and future endemic outbreaks.
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Affiliation(s)
- Ronja Westberg
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Marc Stegger
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Bo Söderquist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Antimicrobial resistance and genomic analysis of staphylococci isolated from livestock and farm attendants in Northern Ghana. BMC Microbiol 2022; 22:180. [PMID: 35864456 PMCID: PMC9306040 DOI: 10.1186/s12866-022-02589-9] [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: 08/02/2021] [Accepted: 07/01/2022] [Indexed: 11/29/2022] Open
Abstract
Background The emergence of antimicrobial resistant bacteria in food producing animals is of growing concern to food safety and health. Staphylococci are common inhabitants of skin and mucous membranes in humans and animals. Infections involving antibiotic resistant staphylococci are associated with increased morbidity and mortality, with notable economic consequences. Livestock farms may enable cross-species transfer of antibiotic resistant staphylococci. The aim of the study was to investigate antimicrobial resistance patterns of staphylococci isolated from livestock and farm attendants in Northern Ghana using phenotypic and genotypic methods. Antimicrobial susceptibility testing was performed on staphylococci recovered from livestock and farm attendants and isolates resistant to cefoxitin were investigated using whole genome sequencing. Results One hundred and fifty-two staphylococci comprising S. sciuri (80%; n = 121), S. simulans (5%; n = 8), S. epidermidis (4%; n = 6), S. chromogens (3%; n = 4), S. aureus (2%; n = 3), S. haemolyticus (1%; n = 2), S. xylosus (1%; n = 2), S. cohnii (1%; n = 2), S. condimenti (1%; n = 2), S. hominis (1%; n = 1) and S. arlettae (1%; n = 1) were identified. The isolates showed resistance to penicillin (89%; n = 135), clindamycin (67%; n = 102), cefoxitin (19%; n = 29), tetracycline (15%; n = 22) and erythromycin (11%; n = 16) but showed high susceptibility to gentamicin (96%; n = 146), sulphamethoxazole/trimethoprim (98%; n = 149) and rifampicin (99%; n = 151). All staphylococci were susceptible to linezolid and amikacin. Carriage of multiple resistance genes was common among the staphylococcal isolates. Genome sequencing of methicillin (cefoxitin) resistant staphylococci (MRS) isolates revealed majority of S. sciuri (93%, n = 27) carrying mecA1 (which encodes for beta-lactam resistance) and the sal(A) gene, responsible for resistance to lincosamide and streptogramin. Most of the MRS isolates were recovered from livestock. Conclusion The study provides insights into the genomic content of MRS from farm attendants and livestock in Ghana and highlights the importance of using whole-genome sequencing to investigate such opportunistic pathogens. The finding of multi-drug resistant staphylococci such as S. sciuri carrying multiple resistant genes is of public health concern as they could pose a challenge for treatment of life-threatening infections that they may cause.
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