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Slotved HC, Johannesen TB, Stegger M, Dalby T, Fuursted K. National Danish surveillance of invasive clinical Haemophilus influenzae isolates and their resistance profile. Front Microbiol 2023; 14:1307261. [PMID: 38075872 PMCID: PMC10702724 DOI: 10.3389/fmicb.2023.1307261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/07/2023] [Indexed: 06/29/2024] Open
Abstract
INTRODUCTION This study aimed to investigate the epidemiology, serotype distribution, phenotypical antibiogram, and molecular resistance gene characteristics of invasive Haemophilus influenzae infections in Denmark from 2014 to 2022. Additionally, the potential impact of outdoor temperature and COVID-19 restrictions on the epidemiology of H. influenzae was assessed. MATERIALS AND METHODS Invasive H. influenzae isolates were received from patients with positive culture results from cerebrospinal fluid, blood, or other sterile sites. Sample data were obtained from the Danish laboratory surveillance system/MiBa database, and whole-genome sequencing (WGS) was performed on the isolates. The incidence rates and distribution of H. influenzae cases were analyzed, and antibiotic susceptibility were assessed. RESULTS A total of 1,007 invasive H. influenzae cases were identified, with serotyping conducted for 752 (74.7%) isolates. The median incidence per year of H. influenzae was 2.0 cases per 100,000, with the highest incidence in 2014 and the lowest in 2020. The majority of H. influenzae isolates were non-typeable H. influenzae (NTHi), while the most prominent serotypes were serotype f followed by serotype b. Bacteremia cases accounted for the majority (88.6%) of occurrences, although meningitis cases showed an increasing trend during the time period. The age group 85+ exhibited the highest incidence. The implementation of COVID-19 preventive interventions in 2020 resulted in a significant reduction in H. influenzae incidence, which returned to pre-COVID levels in 2021. A negative correlation was observed between monthly H. influenzae cases and outdoor temperature. An overall level of genetic beta-lactamase resistance of 26.3% was observed divided into 10.6% beta-lactamase-positive ampicillin-resistant (gBLPAR), 13.6% beta-lactamase-negative ampicillin-resistant (gBLNAR) and 2.1% beta-lactamase-positive amoxicillin clavulanate-resistant (gBLPACR). Other non-beta-lactam resistance traits were detected in 7.6% of isolates (primarily aminoglycoside-modifying enzymes). CONCLUSION The overall incidence of H. influenzae in Denmark returned to stable levels after the COVID-19 epidemic, with NTHi strains dominating. The COVID-19 preventive interventions led to a major reduction in incidence. A significant negative correlation between the incidence of H. influenzae and temperature was observed. The study revealed an overall genetic beta-lactam resistance rate of 26.3%, and the concordance between genotypic and phenotypic beta-lactam resistance was high (98.2%).
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Affiliation(s)
- Hans-Christian Slotved
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Tine Dalby
- Department of Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Kurt Fuursted
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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Founou LL, Khan UB, Medugu N, Pinto TCA, Darboe S, Chendi Z, Founou RC, To KN, Jamrozy D, Karampatsas K, Carr VR, Pepper K, Dangor Z, Ip M, Le Doare K, Bentley SD. Molecular epidemiology of Streptococcus agalactiae in non-pregnant populations: a systematic review. Microb Genom 2023; 9. [PMID: 38019122 DOI: 10.1099/mgen.0.001140] [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] [Indexed: 11/30/2023] Open
Abstract
Streptococcus agalactiae (group B Streptococcus, GBS) has recently emerged as an important pathogen among adults. However, it is overlooked in this population, with all global efforts being directed towards its containment among pregnant women and neonates. This systematic review assessed the molecular epidemiology and compared how the lineages circulating among non-pregnant populations relate to those of pregnant and neonatal populations worldwide. A systematic search was performed across nine databases from 1 January 2000 up to and including 20 September 2021, with no language restrictions. The Joanna Briggs Institute (JBI) Prevalence Critical Appraisal Tool (PCAT) was used to assess the quality of included studies. The global population structure of GBS from the non-pregnant population was analysed using in silico typing and phylogenetic reconstruction tools. Twenty-four articles out of 13 509 retrieved across 9 databases were eligible. Most studies were conducted in the World Health Organization European region (12/24, 50 %), followed by the Western Pacific region (6/24, 25 %) and the Americas region (6/24, 25 %). Serotype V (23%, 2310/10240) and clonal complex (CC) 1 (29 %, 2157/7470) were the most frequent serotype and CC, respectively. The pilus island PI1 : PI2A combination (29 %, 3931/13751) was the most prevalent surface protein gene, while the tetracycline resistance tetM (55 %, 5892/10624) was the leading antibiotic resistance gene. This study highlights that, given the common serotype distribution identified among non-pregnant populations (V, III, Ia, Ib, II and IV), vaccines including these six serotypes will provide broad coverage. The study indicates advanced molecular epidemiology studies, especially in resource-constrained settings for evidence-based decisions. Finally, the study shows that considering all at-risk populations in an inclusive approach is essential to ensure the sustainable containment of GBS.
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Affiliation(s)
- Luria Leslie Founou
- Reproductive, Maternal, Newborn and Child Health (ReMARCH) Research Unit, Centre of Expertise and Biological Diagnostic of Cameroon Research Institute (CEDBCAM-RI), Yaoundé, Cameroon
- Bioinformatics and Applied Machine Learning Research Unit, EDEN Biosciences Research Institute (EBRI), EDEN Foundation, Yaoundé, Cameroon
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4041, South Africa
| | - Uzma Basit Khan
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Nubwa Medugu
- Department of Medical Microbiology and Parasitology, National Hospital Abuja, Abuja, Nigeria
| | - Tatiana C A Pinto
- Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Saffiatou Darboe
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Zhu Chendi
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, PR China
| | - Raspail Carrel Founou
- Antibiotic Resistance Infectious Diseases (ARID) Research Unit, Centre of Expertise and Biological Diagnostic of Cameroon Research Institute (CEDBCAM-RI), Yaoundé, Cameroon
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4041, South Africa
- Department of Microbiology, Hematology and Immunology, Faculty of Medicine and Pharmaceutical Sciences, University of Dschang, Dschang, Cameroon
| | - Ka-Ning To
- Institute of Infection and Immunity, St George's University of London, London, UK
| | - Dorota Jamrozy
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | | | - Victoria R Carr
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Kevin Pepper
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Ziyaad Dangor
- Vaccines and Infectious Diseases Analytics (VIDA) Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Margaret Ip
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, PR China
| | - Kirsty Le Doare
- Medical Research Council Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Stephen D Bentley
- Department of Pathology, University of Cambridge, Cambridge, UK
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
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Slotved HC, Johannesen TB, Stegger M, Fuursted K. Evaluation of molecular typing for national surveillance of invasive clinical Haemophilus influenzae isolates from Denmark. Front Microbiol 2022; 13:1030242. [PMID: 36466693 PMCID: PMC9712784 DOI: 10.3389/fmicb.2022.1030242] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/24/2022] [Indexed: 08/23/2023] Open
Abstract
Haemophilus influenzae is a gram-negative coccobacillus known to cause respiratory and invasive infections. It can possess a polysaccharide capsule that can be categorized into six different serotypes (i.e., Hia, Hib, Hic, Hid, Hie, and Hif) and non-encapsulated strains that are defined as non-typeable. Furthermore, H. influenzae can be characterized into eight biotypes (I-VIII). Traditionally, isolates have been serotyped and biotyped using phenotypic methods; however, these methods are not always reliable. In this study, we evaluate the use of whole-genome sequencing (WGS) for national surveillance and characterization of clinical Danish H. influenzae isolates. In Denmark, all clinical invasive isolates between 2014 and 2021 have been serotyped using a traditional phenotypic latex agglutination test as well as in silico serotyped using the in silico programs "hinfluenzae_capsule_characterization" and "hicap" to compare the subsequent serotypes. Moreover, isolates were also biotyped using a phenotypic enzyme test and the genomic data for the detection of the genes encoding ornithine, tryptophan, and urease. The results showed a 99-100% concordance between the two genotypic approaches and the phenotypic serotyping, respectively. The biotyping showed a 95% concordance between genotyping and phenotyping. In conclusion, our results show that in a clinical surveillance setting, in silico serotyping and WGS-based biotyping are a robust and reliable approach for typing clinical H. influenzae isolates.
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Affiliation(s)
- Hans-Christian Slotved
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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Li A, Fang M, Hao D, Wu Q, Qian Y, Xu H, Zhu B. Late-Onset Sepsis in a Premature Infant Mediated by Breast Milk: Mother-to-Infant Transmission of Group B Streptococcus Detected by Whole-Genome Sequencing. Infect Drug Resist 2022; 15:5345-5352. [PMID: 36110126 PMCID: PMC9469938 DOI: 10.2147/idr.s381466] [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: 07/15/2022] [Accepted: 09/07/2022] [Indexed: 11/23/2022] Open
Abstract
Background Late-onset group B Streptococcus (LOGBS) sepsis is a cause of infection and death in infants. Infected breast milk has been considered a source of neonatal GBS infection and invasive infection. However, mother-to-infant transmission of GBS detected by the high-resolution diagnostic method is rarely reported. Methods This study describes a low-weight premature infant who developed late-onset GBS septicemia 21 days after birth. GBS strains isolated from the mother’s cervical secretion, the mother’s milk, and the baby’s blood were cultured to identify the source of GBS infection. We further confirmed the GBS isolates through matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS). Finally, we performed whole-genome sequencing (WGS) and phylogenetic analyses on the GBS strains recovered. Results GBS isolates were cultured from the bloodstream of the premature infant and the mother’s milk, respectively. Subsequently, WGS and phylogenetic analyses on three GBS isolates demonstrated that the GBS strain from the infant’s bloodstream was 100% homologous to that from the mother’s breast milk, which had some different gene fragments from the GBS strain from the mother’s cervical secretion. It provided evidence that this infant’s late-onset GBS septicemia originated from his mother’s breast milk instead of the vertical mother-to-infant transmission. Conclusion Through WGS and phylogenetic analysis of the GBS strains, we proved in this study that the late-onset GBS sepsis in a premature infant was derived from his mother’s breast milk. It indicated that WGS diagnosis is an effective tool for infection tracing. Furthermore, this report provides direction for preventing late-onset GBS infection.
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Affiliation(s)
- Aiyun Li
- Department of Clinical Medicine, The Women's Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Ming Fang
- Institute of Infection Disease Control, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Dongjie Hao
- Department of Clinical Medicine, The Women's Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Qiaoai Wu
- Department of Clinical Medicine, The Women's Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Yaqi Qian
- Department of Clinical Medicine, The Women's Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China.,Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, People's Republic of China
| | - Bo Zhu
- Department of Clinical Medicine, The Women's Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
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Chaguza C, Jamrozy D, Bijlsma MW, Kuijpers TW, van de Beek D, van der Ende A, Bentley SD. Population genomics of Group B Streptococcus reveals the genetics of neonatal disease onset and meningeal invasion. Nat Commun 2022; 13:4215. [PMID: 35864107 PMCID: PMC9304382 DOI: 10.1038/s41467-022-31858-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
Group B Streptococcus (GBS), or Streptococcus agalactiae, is a pathogen that causes preterm births, stillbirths, and acute invasive neonatal disease burden and mortality. Here, we investigate bacterial genetic signatures associated with disease onset time and meningeal tissue infection in acute invasive neonatal GBS disease. We carry out a genome-wide association study (GWAS) of 1,338 GBS isolates from newborns with acute invasive disease; the isolates had been collected annually, for 30 years, through a national bacterial surveillance program in the Netherlands. After controlling for the population structure, we identify genetic variation within noncoding and coding regions, particularly the capsule biosynthesis locus, statistically associated with neonatal GBS disease onset time and meningeal invasion. Our findings highlight the impact of integrating microbial population genomics and clinical pathogen surveillance, and demonstrate the effect of GBS genetics on disease pathogenesis in neonates and infants.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA.
| | - Dorota Jamrozy
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Merijn W Bijlsma
- Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Taco W Kuijpers
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory of the Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Paediatric Haematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Diederik van de Beek
- Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology, Amsterdam Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Netherlands Reference Laboratory for Bacterial Meningitis, Center of Infection and Immunity Amsterdam, Amsterdam University Medical Center, Amsterdam, The Netherlands.
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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