1
|
Wilcox RS, Marenda MS, Devlin JM, Wilks CR. Antimicrobial use in laboratory rodent facilities in Australia and New Zealand- a cross-sectional survey of veterinarians and facility managers. PLoS One 2024; 19:e0292908. [PMID: 39178211 PMCID: PMC11343402 DOI: 10.1371/journal.pone.0292908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 04/24/2024] [Indexed: 08/25/2024] Open
Abstract
This cross-sectional study surveyed veterinarians and facility managers to characterise the use of antimicrobials in laboratory rodent facilities within Australia and New Zealand. Most facilities (71%) reported routine administration of antimicrobials. The indications for antibiotic use reflected those described in publications and differed significantly to reasons for use in non-laboratory animals. Antimicrobials used include those of critical importance to human health, and access to these drugs is unregulated, as prescription-only classes are ordered through research catalogues, without human or veterinary physician prescriptions. The ways in which antimicrobials are used in Australian and New Zealand rodent facilities are likely contributing to antimicrobial resistance within rodent populations, particularly as they are largely administered in drinking water, risking subtherapeutic dosing. Much antimicrobial use reported is unnecessary and could be replaced with changes to husbandry and handling. The generation of resistance in both pathogenic and commensal microbes may also represent a work health and safety issue for humans working with these animals. Reported disposal of antimicrobials included discharge into wastewater, without inactivation, and some respondents reported disposal of substrate, or soiled bedding, nesting material, and disposable enrichment items, from treated animals and medicated feed into landfill, without prior inactivation. Environmental contamination with resistant microbes and antimicrobials is a significant driver of antimicrobial resistance. As such, significant opportunities exist to implement judicious and responsible use of antimicrobials within research rodent facilities in Australia and New Zealand, with a particular focus on instituting aseptic surgery, optimising dosing regimens, and inactivation of medicated water and substrate before disposal.
Collapse
Affiliation(s)
- Rebbecca S. Wilcox
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Marc S. Marenda
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Joanne M. Devlin
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Colin R. Wilks
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
2
|
Samarra A, Cabrera-Rubio R, Martínez-Costa C, Collado MC. Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life. Ann Clin Microbiol Antimicrob 2024; 23:72. [PMID: 39138497 PMCID: PMC11323388 DOI: 10.1186/s12941-024-00725-z] [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: 03/05/2024] [Accepted: 07/12/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Alongside microbiota development, the evolution of the resistome is crucial in understanding the early-life acquisition and persistence of Antibiotic Resistance Genes (ARGs). Therefore, the aim of this study is to provide a comprehensive view of the evolution and dynamics of the neonatal resistome from 7 days to 4 months of age using a high-throughput qPCR platform. METHODS In the initial phase, a massive screening of 384 ARGs using a high-throughput qPCR in pooled healthy mother-infant pairs feces from the MAMI cohort was carried out to identify the most abundant and prevalent ARGs in infants and in mothers. This pre-analysis allowed for later targeted profiling in a large number of infants in a longitudinal manner during the first 4 months of life. 16S rRNA V3-V4 amplicon sequencing was performed to asses microbial composition longitudinally. Potential factors influencing the microbiota and ARGs in this period were also considered, such as mode of birth and breastfeeding type. RESULTS Following the massive screening, the top 45 abundant ARGs and mobile genetic elements were identified and studied in 72 infants during their first months of life (7 days, 1, 2, and 4 months). These genes were associated with resistance to aminoglycosides, beta-lactams and tetracyclines, among others, as well as integrons, and other mobile genetic elements. Changes in both ARG composition and quantity were observed during the first 4 months of life: most ARGs abundance increased over time, but mobile genetic elements decreased significantly. Further exploration of modulating factors highlighted the effect on ARG composition of specific microbial genus, and the impact of mode of birth at 7 days and 4 months. The influence of infant formula feeding was observed at 4-month-old infants, who exhibited a distinctive resistome composition. CONCLUSIONS This study illustrates the ARG evolution and dynamics in the infant gut by use of a targeted, high-throughput, quantitative PCR-based method. An increase in antibiotic resistance over the first months of life were observed with a fundamental role of delivery mode in shaping resistance profiles. Further, we highlighted the influence of feeding methods on the resistome development. These findings offer pivotal insights into dynamics of and factors influencing early-life resistome, with potential avenues for intervention strategies.
Collapse
Affiliation(s)
- Anna Samarra
- Departament of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Raúl Cabrera-Rubio
- Departament of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Cecilia Martínez-Costa
- Department of Pediatrics, School of Medicine, University of Valencia, Valencia, Spain
- Pediatric Gastroenterology and Nutrition Section, Hospital Clínico Universitario Valencia, INCLIVA, Valencia, Spain
| | - Maria Carmen Collado
- Departament of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Paterna, Valencia, Spain.
| |
Collapse
|
3
|
Flannery DD, Coggins SA, Medoro AK. Antibiotic Stewardship in the Neonatal Intensive Care Unit. J Intensive Care Med 2024:8850666241258386. [PMID: 38835250 DOI: 10.1177/08850666241258386] [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] [Indexed: 06/06/2024]
Abstract
Antibiotic stewardship is a multidisciplinary, evidence-based approach to optimize antibiotic use and mitigate development of antibiotic resistance. Neonates have high rates of antibiotic exposure, particularly those born preterm and admitted to the NICU, and mounting evidence describes the adverse consequences of such exposures in the absence of infection. Here, we review the general principles of antibiotic stewardship and how they can be applied in NICUs. The unique characteristics of NICUs and patients cared for in this setting, which warrant unique implementation strategies and special considerations are discussed. We summarize current antibiotic use metrics for assessment of responses to stewardship interventions and changes over time, and review evidence-based infection prevention practices in the NICU. Current recommendations for empiric antibiotic use in the NICU and the utility of infection biomarkers are summarized. Lastly, given the growing global threat of increasing antibiotic resistance, specific threats in the NICU are highlighted.
Collapse
Affiliation(s)
- Dustin D Flannery
- Division of Neonatology, Department of Pediatrics, University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah A Coggins
- Division of Neonatology, Department of Pediatrics, University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alexandra K Medoro
- Division of Neonatology, Department of Pediatrics, University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Infectious Diseases, Department of Pediatrics, University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, USA
| |
Collapse
|
4
|
Patangia DV, Grimaud G, O'Shea CA, Ryan CA, Dempsey E, Stanton C, Ross RP. Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome. MICROBIOME 2024; 12:19. [PMID: 38310316 PMCID: PMC10837951 DOI: 10.1186/s40168-023-01732-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/24/2023] [Indexed: 02/05/2024]
Abstract
BACKGROUND Infant gut microbiota is highly malleable, but the long-term longitudinal impact of antibiotic exposure in early life, together with the mode of delivery on infant gut microbiota and resistome, is not extensively studied. METHODS Two hundred and eight samples from 45 infants collected from birth until 2 years of age over five time points (week 1, 4, 8, 24, year 2) were analysed. Based on shotgun metagenomics, the gut microbial composition and resistome profile were compared in the early life of infants divided into three groups: vaginal delivery/no-antibiotic in the first 4 days of life, C-section/no-antibiotic in the first 4 days of life, and C-section/antibiotic exposed in first 4 days of life. Gentamycin and benzylpenicillin were the most commonly administered antibiotics during this cohort's first week of life. RESULTS Newborn gut microbial composition differed in all three groups, with higher diversity and stable composition seen at 2 years of age, compared to week 1. An increase in microbial diversity from week 1 to week 4 only in the C-section/antibiotic-exposed group reflects the effect of antibiotic use in the first 4 days of life, with a gradual increase thereafter. Overall, a relative abundance of Actinobacteria and Bacteroides was significantly higher in vaginal delivery/no-antibiotic while Proteobacteria was higher in C-section/antibiotic-exposed infants. Strains from species belonging to Bifidobacterium and Bacteroidetes were generally persistent colonisers, with Bifidobacterium breve and Bifidobacterium bifidum species being the major persistent colonisers in all three groups. Bacteroides persistence was dominant in the vaginal delivery/no-antibiotic group, with species Bacteroides ovatus and Phocaeicola vulgatus found to be persistent colonisers in the no-antibiotic groups. Most strains carrying antibiotic-resistance genes belonged to phyla Proteobacteria and Firmicutes, with the C-section/antibiotic-exposed group presenting a higher frequency of antibiotic-resistance genes (ARGs). CONCLUSION These data show that antibiotic exposure has an immediate and persistent effect on the gut microbiome in early life. As such, the two antibiotics used in the study selected for strains (mainly Proteobacteria) which were multiple drug-resistant (MDR), presumably a reflection of their evolutionary lineage of historical exposures-leading to what can be an extensive and diverse resistome. Video Abstract.
Collapse
Affiliation(s)
- Dhrati V Patangia
- School of Microbiology, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Ghjuvan Grimaud
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | | | - C A Ryan
- APC Microbiome Ireland, Cork, Ireland
| | - Eugene Dempsey
- APC Microbiome Ireland, Cork, Ireland
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
- Infant Research Centre, University College Cork, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - R Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
| |
Collapse
|
5
|
Gallacher DJ, Zhang L, Aboklaish AF, Mitchell E, Wach R, Marchesi JR, Kotecha S. Baseline azithromycin resistance in the gut microbiota of preterm born infants. Pediatr Res 2024; 95:205-212. [PMID: 37550487 PMCID: PMC10798878 DOI: 10.1038/s41390-023-02743-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Macrolides, including azithromycin, are increasingly used in preterm-born infants to treat Ureaplasma infections. The baseline carriage of macrolide resistance genes in the preterm stool microbiota is unknown. OBJECTIVES Identify carriage of azithromycin resistant bacteria and the incidence of macrolide resistant genes. METHODS Azithromycin resistant bacteria were isolated from serial stool samples obtained from preterm infants (≤32 weeks' gestation) by culturing aerobically/anaerobically, in the presence/absence of azithromycin. Using quantitative PCR, we targeted 6 common macrolide resistance genes (erm(A), erm(B), erm(C), erm(F), mef(A/E), msr(A)) in DNA extracted from selected bacteria resistant to azithromycin. RESULTS From 89 stool samples from 37 preterm-born infants, 93.3% showed bacterial growth in aerobic or anaerobic conditions. From the 280 azithromycin resistant isolates that were identified, Staphylococcus (75%) and Enterococcus (15%) species dominated. Macrolide resistance genes were identified in 91% of resistant isolates: commonest were erm(C) (46% of isolates) and msr(A) (40%). Multiple macrolide resistance genes were identified in 18% of isolates. CONCLUSION Macrolide resistance is common in the gut microbiota of preterm-born infants early in life, most likely acquired from exposure to the maternal microbiota. It will be important to assess modulation of macrolide resistance, if macrolide treatment becomes routine in the management of preterm infants. IMPACT STATEMENT Azithromycin resistance is present in the stool microbiota in the first month of life in preterm infants 91% of azithromycin resistant bacteria carried at least one of 6 common macrolide resistant genes Increasing use of macrolides in the preterm population makes this an important area of study.
Collapse
Affiliation(s)
- David J Gallacher
- Neonatal Unit, University Hospital of Wales, Cardiff, UK
- Department of Child Health, Cardiff University School of Medicine, Cardiff, UK
| | - Lei Zhang
- Department of Child Health, Cardiff University School of Medicine, Cardiff, UK
| | - Ali F Aboklaish
- Department of Child Health, Cardiff University School of Medicine, Cardiff, UK
| | - Emma Mitchell
- Department of Child Health, Cardiff University School of Medicine, Cardiff, UK
| | | | - Julian R Marchesi
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Sailesh Kotecha
- Department of Child Health, Cardiff University School of Medicine, Cardiff, UK.
| |
Collapse
|
6
|
Samarra A, Cabrera-Rubio R, Martínez-Costa C, Collado MC. The role of Bifidobacterium genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life. Gut Microbes 2024; 16:2357176. [PMID: 38798019 PMCID: PMC11135851 DOI: 10.1080/19490976.2024.2357176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
Resistance to antibiotics in newborns is a huge concern as their immune system is still developing, and infections and resistance acquisition in early life have short- and long-term consequences for their health. Bifidobacterium species are important commensals capable of dominating the infant gut microbiome and are known to be less prone to possess antimicrobial resistance genes than other taxa that may colonize infants. We aimed to study the association between Bifidobacterium-dominated infant gut microbiota and the antibiotic resistant gene load in neonates, and to ascertain the perinatal factors that may contribute to the antibiotic resistance acquisition. Two hundred infant fecal samples at 7 days and 1 month of age from the MAMI birth cohort were included in the study and for whom maternal-neonatal clinical records were available. Microbiota profiling was carried out by 16S rRNA amplicon sequencing, and targeted antibiotic resistance genes (ARGs) including tetM, tetW, tetO, blaTEM, blaSHV and ermB were quantified by qPCR. Infant microbiota clustered into two distinct groups according to their Bifidobacterium genus abundance: high and low. The main separation of groups or clusters at each time point was performed with an unsupervised non-linear algorithm of k-means partitioning to cluster data by time points based on Bifidobacterium genus relative abundance. Microbiota composition differed significantly between both groups, and specific bifidobacterial species were enriched in each cluster. Lower abundance of Bifidobacterium in the infant gut was associated with a higher load of antibiotic resistance genes. Our results highlight the relevance of Bifidobacterium genus in the early acquisition and establishment of antibiotic resistance in the gut. Further studies are needed to develop strategies to promote a healthy early colonization and fight against the spread of antibiotic resistances.
Collapse
Affiliation(s)
- Anna Samarra
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Raúl Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Cecilia Martínez-Costa
- Department of Pediatrics, School of Medicine, University of Valencia, Valencia, Spain
- Pediatric Gastroenterology and Nutrition Section, Hospital Clínico Universitario Valencia, Valencia, Spain
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| |
Collapse
|
7
|
Patangia DV, Grimaud G, Wang S, Ross RP, Stanton C. Influence of age, socioeconomic status, and location on the infant gut resistome across populations. Gut Microbes 2024; 16:2297837. [PMID: 38217470 PMCID: PMC10793692 DOI: 10.1080/19490976.2023.2297837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/18/2023] [Indexed: 01/15/2024] Open
Abstract
Antibiotic resistance is a growing global concern, with many ecological niches showing a high abundance of antibiotic resistance genes (ARGs), including the human gut. With increasing indications of ARGs in infants, this study aims to investigate the gut resistome profile during early life at a wider geographic level. To achieve this objective, we utilized stool samples data from 26 studies involving subjects aged up to 3 years from different geographical locations. The 32,277 Metagenome Assembled Genomes (MAGs) previously generated from shotgun sequencing reads from these studies were used for resistome analysis using RGI with the CARD database. This analysis showed that the distribution of ARGs across the countries in our study differed in alpha diversity and compositionally. In particular, the abundance of ARGs was found to vary by socioeconomic status and healthcare access and quality (HAQ) index. Surprisingly, countries having lower socioeconomic status and HAQ indices showed lower ARG abundance, which was contradictory to previous reports. Gram-negative genera, including Escherichia, Enterobacter, Citrobacter, and Klebsiella harbored a particularly rich set of ARGs, which included antibiotics that belong to the Reserve, Access or Watch category, such as glycopeptides, fluoroquinolones, sulfonamides, macrolides, and tetracyclines. We showed that ARG abundance exponentially decreased with time during the first 3 years of life. Many highly ARG-abundant species including Escherichia, Klebsiella, Citrobacter species that we observed are well-known pathobionts found in the infant gut in early life. High abundance of these species and a diverse range of ARGs in their genomes point toward the infant gut, acting as an ARG reservoir. This is a concern and further studies are needed to examine the causal effect and its consequences on long-term health.
Collapse
Affiliation(s)
- Dhrati V. Patangia
- School of Microbiology, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Ghjuvan Grimaud
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Shaopu Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - R. Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| |
Collapse
|
8
|
Saturio S, Rey A, Samarra A, Collado MC, Suárez M, Mantecón L, Solís G, Gueimonde M, Arboleya S. Old Folks, Bad Boon: Antimicrobial Resistance in the Infant Gut Microbiome. Microorganisms 2023; 11:1907. [PMID: 37630467 PMCID: PMC10458625 DOI: 10.3390/microorganisms11081907] [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: 06/15/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
The development of the intestinal microbiome in the neonate starts, mainly, at birth, when the infant receives its founding microbial inoculum from the mother. This microbiome contains genes conferring resistance to antibiotics since these are found in some of the microorganisms present in the intestine. Similarly to microbiota composition, the possession of antibiotic resistance genes is affected by different perinatal factors. Moreover, antibiotics are the most used drugs in early life, and the use of antibiotics in pediatrics covers a wide variety of possibilities and treatment options. The disruption in the early microbiota caused by antibiotics may be of great relevance, not just because it may limit colonization by beneficial microorganisms and increase that of potential pathogens, but also because it may increase the levels of antibiotic resistance genes. The increase in antibiotic-resistant microorganisms is one of the major public health threats that humanity has to face and, therefore, understanding the factors that determine the development of the resistome in early life is of relevance. Recent advancements in sequencing technologies have enabled the study of the microbiota and the resistome at unprecedent levels. These aspects are discussed in this review as well as some potential interventions aimed at reducing the possession of resistance genes.
Collapse
Affiliation(s)
- Silvia Saturio
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.S.); (A.R.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
| | - Alejandra Rey
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.S.); (A.R.)
| | - Anna Samarra
- Institute of Agrochemistry and Food Technology (IATA-CSIC), 46980 Paterna, Spain; (A.S.); (M.C.C.)
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology (IATA-CSIC), 46980 Paterna, Spain; (A.S.); (M.C.C.)
| | - Marta Suárez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
| | - Laura Mantecón
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
| | - Gonzalo Solís
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
| | - Miguel Gueimonde
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.S.); (A.R.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
| | - Silvia Arboleya
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.S.); (A.R.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
| |
Collapse
|
9
|
Samarra A, Esteban-Torres M, Cabrera-Rubio R, Bernabeu M, Arboleya S, Gueimonde M, Collado MC. Maternal-infant antibiotic resistance genes transference: what do we know? Gut Microbes 2023; 15:2194797. [PMID: 37020319 PMCID: PMC10078139 DOI: 10.1080/19490976.2023.2194797] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023] Open
Abstract
Resistance to antibiotics is becoming a worldwide threat as infections caused by multidrug-resistant pathogenic microorganisms can overcome antibiotic treatments and spread quickly in the population. In the context of early life, newborns are at increased risk as their immune system is still under development, so infections and acquisition of resistance during childhood have short- and long-term consequences for the health. The moment of birth is the first exposure of infants to possible antibiotic-resistant microorganisms that may colonize their gut and other body sites. Different factors including mode of delivery, previous antibiotic exposure of the mother, gestational age and consumption of antibiotics in early-life have been described to modulate the neonate's microbiota, and thus, the resistome. Other factors, such as lactation, also impact the establishment and development of gut microbiota, but little is known about the role of breastmilk in transferring Antibiotic Resistant Genes (ARG). A deeper understanding of vertical transmission of antibiotic resistance from mothers to their offspring is necessary to determine the most effective strategies for reducing antibiotic resistance in the early life. In this review, we aim to present the current perspective on antibiotic resistances in mother-infant dyads, as well as a new insight on the study of the human gut and breastmilk resistome, and current strategies to overcome this public health problem, toward highlighting the gaps of knowledge that still need to be closed.
Collapse
Affiliation(s)
- Anna Samarra
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Valencia, Spain
| | - Maria Esteban-Torres
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Valencia, Spain
| | - Raul Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Valencia, Spain
| | - Manuel Bernabeu
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Valencia, Spain
- Vicerectorat de Recerca, Universitat de Barcelona (UB), Barcelona, Spain
| | - Silvia Arboleya
- Department of Microbiology and Biochemistry, Dairy Research Institute- National Research Council (IPLA-CSIC), Villaviciosa, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry, Dairy Research Institute- National Research Council (IPLA-CSIC), Villaviciosa, Spain
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Valencia, Spain
| |
Collapse
|
10
|
Gospodaryk AV, Ulakhanova LA, Esiev SS, Polyakova EV, Shansky YD, Bespyatykh JA. The role of mef and ermB drug resistance genetic markers in the selection of fecal microbiota donors. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2022. [DOI: 10.24075/brsmu.2022.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fecal microbiota transplantation (FMT) is prescribed to treat various gastrointestinal pathologies. One of the most important and significant stages of FMT is selection of the donor. In recent years, special attention has been paid to checking the biomaterial for genes marking resistance to various groups of antibiotics. This study aimed to analyze the occurrence of mef and ermB drug resistance genetic markers in population of various age groups, including breastfed infants, and to determine microbiological composition of the flora of distal part of the intestine of potentially healthy volunteering FMT donors. A total of 52 biological samples (46 stool samples and 6 breast milk samples) were analyzed by real-time polymerase chain reaction. The macrolides resistance gene (mef) was detected in 97.8% of stool samples (different age groups), the gene marking resistance to macrolides, lincosamides, streptogramin (ermB) — in 93.5%. In the isolated "mother-child" group, the mef gene was found in all samples of breast milk and feces. The ermB gene in this group was found in 3 out of 6 breast milk samples and 4 out of 6 infant stool samples. Since the mef and ermB genetic determinants were identified not only among in adults but also in infants, it was suggested that transplant material (feces) containing these genes can be used for FMT. The analysis of microbiological composition of stool samples from 23 healthy volunteers (potential FMT donors) revealed that it rarely (in 8.7% of cases only) corresponds to what is considered to be a normal microbiota of the intestine's distal part.
Collapse
Affiliation(s)
- AV Gospodaryk
- Lopukhin Federal Research and Clinical Center Of Physical-Chemical Medicine under the Federal Medical Biological Agency, Moscow, Russia
| | - LA Ulakhanova
- Lopukhin Federal Research and Clinical Center Of Physical-Chemical Medicine under the Federal Medical Biological Agency, Moscow, Russia
| | - SS Esiev
- Lopukhin Federal Research and Clinical Center Of Physical-Chemical Medicine under the Federal Medical Biological Agency, Moscow, Russia
| | - EV Polyakova
- Lopukhin Federal Research and Clinical Center Of Physical-Chemical Medicine under the Federal Medical Biological Agency, Moscow, Russia
| | - YD Shansky
- Lopukhin Federal Research and Clinical Center Of Physical-Chemical Medicine under the Federal Medical Biological Agency, Moscow, Russia
| | - JA Bespyatykh
- Lopukhin Federal Research and Clinical Center Of Physical-Chemical Medicine under the Federal Medical Biological Agency, Moscow, Russia
| |
Collapse
|
11
|
Gaire TN, Odland C, Zhang B, Ray T, Doster E, Nerem J, Dee S, Davies P, Noyes N. The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs. MICROBIOME 2022; 10:118. [PMID: 35922873 PMCID: PMC9351240 DOI: 10.1186/s40168-022-01312-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Antimicrobials are used in food-producing animals for purposes of preventing, controlling, and/or treating infections. In swine, a major driver of antimicrobial use is porcine reproductive and respiratory syndrome (PRRS), which is caused by a virus that predisposes infected animals to secondary bacterial infections. Numerous antimicrobial protocols are used to treat PRRS, but we have little insight into how these treatment schemes impact antimicrobial resistance (AMR) dynamics within the fecal microbiome of commercial swine. The aim of this study was to determine whether different PRRS-relevant antimicrobial treatment protocols were associated with differences in the fecal microbiome and resistome of growing pigs. To accomplish this, we used a metagenomics approach to characterize and compare the longitudinal wean-to-market resistome and microbiome of pigs challenged with PRRS virus and then exposed to different antimicrobial treatments, and a group of control pigs not challenged with PRRS virus and having minimal antimicrobial exposure. Genomic DNA was extracted from pen-level composite fecal samples from each treatment group and subjected to metagenomic sequencing and microbiome-resistome bioinformatic and statistical analysis. Microbiome-resistome profiles were compared over time and between treatment groups. RESULTS Fecal microbiome and resistome compositions both changed significantly over time, with a dramatic and stereotypic shift between weaning and 9 days post-weaning (dpw). Antimicrobial resistance gene (ARG) richness and diversity were significantly higher at earlier time points, while microbiome richness and diversity were significantly lower. The post-weaning shift was characterized by transition from a Bacteroides-dominated enterotype to Lactobacillus- and Streptococcus-dominated enterotypes. Both the microbiome and resistome stabilized by 44 dpw, at which point the trajectory of microbiome-resistome maturation began to diverge slightly between the treatment groups, potentially due to physical clustering of the pigs. Challenge with PRRS virus seemed to correspond to the re-appearance of many very rare and low-abundance ARGs within the feces of challenged pigs. Despite very different antimicrobial exposures after challenge with PRRS virus, resistome composition remained largely similar between the treatment groups. Differences in ARG abundance between the groups were mostly driven by temporal changes in abundance that occurred prior to antimicrobial exposures, with the exception of ermG, which increased in the feces of treated pigs, and was significantly more abundant in the feces of these pigs compared to the pigs that did not receive post-PRRS antimicrobials. CONCLUSIONS The fecal microbiome-resistome of growing pigs exhibited a stereotypic trajectory driven largely by weaning and physiologic aging of the pigs. Events such as viral illness, antimicrobial exposures, and physical grouping of the pigs exerted significant yet relatively minor influence over this trajectory. Therefore, the AMR profile of market-age pigs is the culmination of the life history of the individual pigs and the populations to which they belong. Disease status alone may be a significant driver of AMR in market-age pigs, and understanding the interaction between disease processes and antimicrobial exposures on the swine microbiome-resistome is crucial to developing effective, robust, and reproducible interventions to control AMR. Video Abstract.
Collapse
Affiliation(s)
- Tara N Gaire
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Carissa Odland
- Pipestone Veterinary Services, Pipestone, Minnesota, USA
| | - Bingzhou Zhang
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tui Ray
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Enrique Doster
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Joel Nerem
- Pipestone Applied Research, Pipestone, Minnesota, USA
| | - Scott Dee
- Pipestone Applied Research, Pipestone, Minnesota, USA
| | - Peter Davies
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Noelle Noyes
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA.
| |
Collapse
|
12
|
Leo S, Curtis N, Zimmermann P. The neonatal intestinal resistome and factors that influence it - a systematic review. Clin Microbiol Infect 2022; 28:1539-1546. [PMID: 35868586 DOI: 10.1016/j.cmi.2022.07.014] [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: 05/17/2022] [Revised: 06/21/2022] [Accepted: 07/14/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND The intestinal microbiome provides a reservoir for antibiotic resistance genes (ARGs). The neonatal microbiome is more susceptible to disturbance from external factors than the established microbiome. OBJECTIVES In this review, we systematically summarise studies which investigated the intestinal resistome in neonates. DATA SOURCES MEDLINE and Embase databases were searched. STUDY ELIGIBILITY CRITERIA We included original studies which investigated ARGs in stool or rectal swabs in neonates using molecular diagnostics. METHODS OF DATA SYNTHESIS Two authors independently extracted data. Data was summarised in tables. RESULTS Our search identified 2,701 studies, of which 23 (22 cohorts) were included. The studies show that the neonatal intestine harbours a high abundance and variety of ARGs, even in the absence of direct antibiotic exposure. The most-commonly found ARGs confer resistance to aminoglycosides, beta-lactams, macrolides, tetracyclines or multi-drug resistance. There is evidence that ARGs can be transferred from mothers to neonates. Interestingly, however, compared to mothers, neonates are reported to have a higher abundance of ARGs. One likely reason for this is the bacterial phylogenetic composition with a high abundance of Gammaproteobacteria in neonatal stool. Factors that have been associated with a higher abundance of ARGs are intrapartum and neonatal antibiotic use. Breastfeeding and neonatal probiotic use have been associated with a lower abundance of ARGs. Antibiotics during pregnancy, delivery mode or sex are reported to have little effect. However, this might be because studies were underpowered and because it is difficult to account for effect modifiers. DISCUSSION The neonatal intestine seems to have a lower colonisation resistance, which could make it easier for antibiotic-resistant populations to establish themselves. Future studies will help in the development of evidence-based interventions to modulate the abundance of ARGs in neonates, for example, by the use of pre- and probiotics and bacteriophages.
Collapse
Affiliation(s)
- Stefano Leo
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland
| | - Nigel Curtis
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Australia
| | - Petra Zimmermann
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland; Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia.
| |
Collapse
|
13
|
Klassert TE, Zubiria-Barrera C, Neubert R, Stock M, Schneegans A, López M, Driesch D, Zakonsky G, Gastmeier P, Slevogt H, Leistner R. Comparative analysis of surface sanitization protocols on the bacterial community structures in the hospital environment. Clin Microbiol Infect 2022; 28:1105-1112. [PMID: 35272014 DOI: 10.1016/j.cmi.2022.02.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/10/2022] [Accepted: 02/20/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVES In hospital hygiene it remains unclear to which extent surface contamination might represent a potential reservoir for nosocomial pathogens. This study investigates the effects of different sanitization strategies on the microbial structures and the ecological balance of the environmental microbiome in the clinical setting. METHODS Three cleaning regimes (disinfectants, detergents and probiotics) were applied subsequently in 9 independent patient rooms at a neurological ward (Charité, Berlin). Weekly sampling procedures included 3 different environmental sites: floor, doorhandle and sink. Characterization of the environmental microbiota and detection of antibiotic resistance genes (ARGs) were performed by 16S rRNA sequencing and multiplex Taq-Man qPCR assays, respectively. RESULTS Our results showed a displacement of the intrinsic environmental microbiota after probiotic sanitization, which reached statistical significance in the sink samples (Median 16S-rRNA copies = 138.3; IQR: 24.38-379.5) when compared to traditional disinfection measures (Median 16S-rRNA copies = 1343; IQR: 330.9-9479; p<0.05). This effect was concomitant with a significant increase of the alpha-diversity metrics in both the floor (p<0.001) and the sink samples (p<0.01) during the probiotic strategy. We did not observe a sanitization-dependent change of relative pathogen abundance at any tested site, but a significant reduction of the total ARGs counts in the sink samples during probiotic cleaning (mean ARGs/sample: 0.095 ± 0.067) when compared to the disinfection strategy (mean ARGs/sample: 0.386 ± 0.116; p<0.01). CONCLUSIONS The data presented in this study suggest the probiotic sanitization as interesting strategy in hospital hygiene management to be further analyzed and validated in randomized clinical studies.
Collapse
Affiliation(s)
- Tilman E Klassert
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany.
| | | | - Robert Neubert
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany
| | - Magdalena Stock
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany
| | - Antony Schneegans
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany
| | - Mercedes López
- University Institute of Tropical Diseases and Public Health of the Canary Islands, University of La Laguna, Spain
| | | | | | - Petra Gastmeier
- Institute for Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Germany
| | - Hortense Slevogt
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany; Department of Respiratory Medicine, Medizinische Hochschule Hannover, Germany
| | - Rasmus Leistner
- Institute for Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Germany
| |
Collapse
|
14
|
Bossung V, Lupatsii M, Dashdorj L, Tassiello O, Jonassen S, Pagel J, Demmert M, Wolf EA, Rody A, Waschina S, Graspeuntner S, Rupp J, Härtel C. Timing of antimicrobial prophylaxis for cesarean section is critical for gut microbiome development in term born infants. Gut Microbes 2022; 14:2038855. [PMID: 35184691 PMCID: PMC8865290 DOI: 10.1080/19490976.2022.2038855] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Animal models imply that the perinatal exposure to antibiotics has a substantial impact on microbiome establishment of the offspring. We aimed to evaluate the effect of timing of antimicrobial prophylaxis for cesarean section before versus after cord clamping on gut microbiome composition of term born infants. We performed an exploratory, single center randomized controlled clinical trial. We included forty pregnant women with elective cesarean section at term. The intervention group received single dose intravenous cefuroxime after cord clamping (n = 19), the control group single dose intravenous cefuroxime 30 minutes before skin incision (n = 21). The primary endpoint was microbiome signature of infants and metabolic prediction in the first days of life as determined in meconium samples by 16S rRNA gene sequencing. Secondary endpoints were microbiome composition at one month and 1 year of life. In meconium samples of the intervention group, the genus Staphylococcus pre-dominated. In the control group, the placental cross-over of cefuroxime was confirmed in cord blood. A higher amino acid and nitrogen metabolism as well as increased abundance of the genera Cutibacterium, Corynebacterium and Streptophyta were noted (indicator families: Cytophagaceae, Lactobacilaceae, Oxalobacteraceae). Predictive models of metabolic function revealed higher 2'fucosyllactose utilization in control group samples. In the follow-up visits, a higher abundance of the genus Clostridium was evident in the intervention group. Our exploratory randomized controlled trial suggests that timing of antimicrobial prophylaxis is critical for early microbiome engraftment but not antimicrobial resistance emergence in term born infants.
Collapse
Affiliation(s)
- Verena Bossung
- Department of Obstetrics and Gynecology, University Hospital of Schleswig-Holstein, Campus, Lübeck, Germany
| | - Mariia Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | | | - Oronzo Tassiello
- Institute for Human Nutrition and Food Science, Nutriinformatics, University of Kiel, Kiel, Germany
| | - Sinje Jonassen
- Department of Obstetrics and Gynecology, University Hospital of Schleswig-Holstein, Campus, Lübeck, Germany
| | - Julia Pagel
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
- Department of Pediatrics, University Hospital of Schleswig-Holstein, Campus, Lübeck, Germany
| | - Martin Demmert
- Department of Pediatrics, University Hospital of Schleswig-Holstein, Campus, Lübeck, Germany
| | - Ellinor Anna Wolf
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Achim Rody
- Department of Obstetrics and Gynecology, University Hospital of Schleswig-Holstein, Campus, Lübeck, Germany
| | - Silvio Waschina
- Institute for Human Nutrition and Food Science, Nutriinformatics, University of Kiel, Kiel, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Christoph Härtel
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
- Department of Pediatrics, University Hospital of Schleswig-Holstein, Campus, Lübeck, Germany
- Department of Pediatrics, University Hospital of Würzburg, Wurzburg, Germany
| |
Collapse
|
15
|
Klassert TE, Leistner R, Zubiria-Barrera C, Stock M, López M, Neubert R, Driesch D, Gastmeier P, Slevogt H. Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study. MICROBIOME 2021; 9:169. [PMID: 34380550 PMCID: PMC8359561 DOI: 10.1186/s40168-021-01109-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/02/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Humans spend the bulk of their time in indoor environments. This space is shared with an indoor ecosystem of microorganisms, which are in continuous exchange with the human inhabitants. In the particular case of hospitals, the environmental microorganisms may influence patient recovery and outcome. An understanding of the bacterial community structure in the hospital environment is pivotal for the prevention of hospital-acquired infections and the dissemination of antibiotic resistance genes. In this study, we performed a longitudinal metagenetic approach in a newly opened ward at the Charité Hospital (Berlin) to characterize the dynamics of the bacterial colonization process in the hospital environment after first patient occupancy. RESULTS The sequencing data showed a site-specific taxonomic succession, which led to stable community structures after only a few weeks. This data was further supported by network analysis and beta-diversity metrics. Furthermore, the fast colonization process was characterized by a significant increase of the bacterial biomass and its alpha-diversity. The compositional dynamics could be linked to the exchange with the patient microbiota. Over a time course of 30 weeks, we did not detect a rise of pathogenic bacteria in the hospital environment, but a significant increase of antibiotic resistance determinants on the hospital floor. CONCLUSIONS The results presented in this study provide new insights into different aspects of the environmental microbiome in the clinical setting, and will help to adopt infection control strategies in hospitals and health care-related buildings. Video Abstract.
Collapse
Affiliation(s)
- Tilman E Klassert
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany.
| | - Rasmus Leistner
- Institute for Hygiene and Environmental Medicine and Department for Medicine (Gastroenterology, Infectious diseases, Rheumatology), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Magdalena Stock
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany
| | - Mercedes López
- University Institute of Tropical Diseases and Public Health of the Canary Islands, University of La Laguna, San Cristóbal de La Laguna, Spain
| | - Robert Neubert
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany
| | | | - Petra Gastmeier
- Institute for Hygiene and Environmental Medicine, Charité-Universitätsmedizin, Berlin, Germany
| | - Hortense Slevogt
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany
| |
Collapse
|
16
|
Zubiria-Barrera C, Stock M, Neubert R, Vester A, Kulle A, Schneegans A, Leistner R, Gastmeier P, Slevogt H, Klassert TE. A simple sequence-based filtering method for the removal of contaminants in low-biomass 16S rRNA amplicon sequencing approaches. J Microbiol Methods 2020; 178:106060. [PMID: 32949682 DOI: 10.1016/j.mimet.2020.106060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/13/2020] [Accepted: 09/13/2020] [Indexed: 02/08/2023]
Abstract
Controlling for contaminant sequences in microbiome experiments involving low-biomass samples is a highly challenging task which still lacks of standardized protocols. Here we propose a simple sequence-based filtering method for 16S rRNA gene microbial profiling approaches, and validate its efficiency using mock community dilution series and environmental samples collected in a clinical setting.
Collapse
Affiliation(s)
- Cristina Zubiria-Barrera
- Jena University Hospital, ZIK Septomics, Host Septomics, Albert-Einstein-Str. 10, Jena 07745, Germany
| | - Magdalena Stock
- Jena University Hospital, ZIK Septomics, Host Septomics, Albert-Einstein-Str. 10, Jena 07745, Germany
| | - Robert Neubert
- Jena University Hospital, ZIK Septomics, Host Septomics, Albert-Einstein-Str. 10, Jena 07745, Germany
| | - Antje Vester
- Jena University Hospital, ZIK Septomics, Host Septomics, Albert-Einstein-Str. 10, Jena 07745, Germany
| | - Aylina Kulle
- Jena University Hospital, ZIK Septomics, Host Septomics, Albert-Einstein-Str. 10, Jena 07745, Germany
| | - Antony Schneegans
- Jena University Hospital, ZIK Septomics, Host Septomics, Albert-Einstein-Str. 10, Jena 07745, Germany
| | - Rasmus Leistner
- Charité Universitätsmedizin Berlin, Institut für Hygiene und Umweltmedizin, Hindenburgdamm 27, Berlin 12203, Germany
| | - Petra Gastmeier
- Charité Universitätsmedizin Berlin, Institut für Hygiene und Umweltmedizin, Hindenburgdamm 27, Berlin 12203, Germany
| | - Hortense Slevogt
- Jena University Hospital, ZIK Septomics, Host Septomics, Albert-Einstein-Str. 10, Jena 07745, Germany
| | - Tilman E Klassert
- Jena University Hospital, ZIK Septomics, Host Septomics, Albert-Einstein-Str. 10, Jena 07745, Germany.
| |
Collapse
|