Horizontal Gene Transfer and Acquired Antibiotic Resistance in Salmonella enterica Serovar Heidelberg following In Vitro Incubation in Broiler Ceca

ABSTRACT The chicken gastrointestinal tract harbors microorganisms that play a role in the health and disease status of the host. The cecum is the part of the gut that carries the highest microbial densities, has the longest residence time of digesta, and is a vital site for urea recycling and water regulation. Therefore, the cecum provides a rich environment for bacteria to horizontally transfer genes between one another via mobile genetic elements such as plasmids and bacteriophages. In this study, we used broiler chicken cecum as a model to investigate antibiotic resistance genes that can be transferred in vitro from cecal flora to Salmonella enterica serovar Heidelberg. We used whole-genome sequencing and resistome enrichment to decipher the interactions between S. Heidelberg, the gut microbiome, and acquired antibiotic resistance. After 48 h of incubation of ceca under microaerophilic conditions, we recovered one S. Heidelberg isolate with an acquired IncK2 plasmid (88 kb) carrying an extended-spectrum-β-lactamase gene (blaCMY-2). In vitro, this plasmid was transferable between Escherichia coli and S. Heidelberg strains but transfer was unsuccessful between S. Heidelberg strains. An in-depth genetic characterization of transferred plasmids suggests that they share significant homology with P1-like phages. This study contributes to our understanding of horizontal gene transfer between an important foodborne pathogen and the chicken gut microbiome. IMPORTANCE S. Heidelberg is a clinically important serovar, linked to foodborne illness and among the top 5 serovars isolated from poultry in the United States and Canada. Acquisition of new genetic material from the microbial flora in the gastrointestinal tract of food animals, including broilers, may contribute to increased fitness of pathogens like S. Heidelberg and may increase their level of antibiotic tolerance. Therefore, it is critical to gain a better understanding of the interactions that occur between important pathogens and the commensals present in the animal gut and other agroecosystems. In this report, we show that the native flora in broiler ceca were capable of transferring mobile genetic elements carrying the AmpC β-lactamase (blaCMY-2) gene to an important foodborne pathogen, S. Heidelberg. The potential role for bacteriophage transduction is also discussed.

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Dynamics between horizontal gene transfer and acquired antibiotic resistance in S. Heidelberg following in vitro incubation in broiler ceca

10.1101/684787 ◽

2019 ◽

Author(s):

Adelumola Oladeinde ◽

Kimberly Cook ◽

Steven M. Lakin ◽

Zaid Abdo ◽

Torey Looft ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gastrointestinal Tract ◽

Gut Microbiome ◽

Genetic Material ◽

Mobile Genetic Elements ◽

Important Food ◽

Genetic Elements ◽

Food Borne ◽

Acquired Antibiotic Resistance

AbstractThe chicken gastrointestinal tract harbors taxa of microorganisms that play a role in the health and disease status of the host. The cecum is the part of the gut that carries the highest microbial densities, has the longest residence time of digesta and is a vital site for urea recycling and water regulation. Therefore, the cecum provides a rich environment for bacteria to horizontally transfer genes between one another via mobile genetic elements such as plasmids and bacteriophages. In this study, we used broiler chicken cecum as a model to investigate antibiotic resistance genes that can be transferred in vitro from ceca flora to Salmonella enterica serovar Heidelberg (S. Heidelberg). We used whole genome sequencing and resistome enrichment to decipher the interactions between S. Heidelberg, gut microbiome and acquired antibiotic resistance. After 48 h incubation of ceca under microaerophilic conditions, one S. Heidelberg isolate was recovered with an acquired Inck2 plasmid (88 kb) encoding extended β-lactamase producing gene (blaCMY-2). In vitro, this plasmid was transferrable between E. coli and S. Heidelberg strains, but transfer was unsuccessful between S. Heidelberg strains. An in-depth genetic characterization of transferred plasmids suggests that they share significant homology with P1-like phages. This study contributes to our understanding of the dynamics between an important food-borne pathogen and the chicken gut microbiome.ImportanceS. Heidelberg is a clinically important serovar, linked to food-borne illness and among the top 5 serovars isolated from poultry in USA and Canada. Acquisition of new genetic material from microbial flora in the gastrointestinal tract of food animals, including broilers, may contribute to increased fitness of pathogens like S. Heidelberg and may increase their level of antibiotic tolerance. Therefore, it is critical to gain a better understanding on the dynamic interactions that occur between important pathogens and the commensals present in the animal gut and other agroecosystems. In this study, we show that the native flora in the broiler ceca were capable of transferring mobile genetic elements carrying AmpC β-lactamase (blaCMY-2) gene to an important food-borne pathogen S. Heidelberg. The potential role for P1-like bacteriophage transduction was also discussed.

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Horizontal Gene Transfer of Antibiotic Resistance from Acinetobacter baylyi to Escherichia coli on Lettuce and Subsequent Antibiotic Resistance Transmission to the Gut Microbiome

mSphere ◽

10.1128/msphere.00329-20 ◽

2020 ◽

Vol 5 (3) ◽

Cited By ~ 2

Author(s):

Marlène Maeusli ◽

Bosul Lee ◽

Sarah Miller ◽

Zeferino Reyna ◽

Peggy Lu ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Resistance Genes ◽

Gut Microbiome ◽

Acinetobacter Baylyi ◽

Antibiotic Resistant ◽

Content Type ◽

Plant Foods ◽

Link Type

ABSTRACT Agricultural use of antibiotics is recognized by the U.S. Centers for Disease Control and Prevention as a major contributor to antibiotic-resistant infections. While most One Health attention has been on the potential for antibiotic resistance transmission from livestock and contaminated meat products to people, plant foods are fundamental to the food chain for meat eaters and vegetarians alike. We hypothesized that environmental bacteria that colonize plant foods may serve as platforms for the persistence of antibiotic-resistant bacteria and for horizontal gene transfer of antibiotic-resistant genes. Donor Acinetobacter baylyi and recipient Escherichia coli were cocultured in vitro, in planta on lettuce, and in vivo in BALB/c mice. We showed that nonpathogenic, environmental A. baylyi is capable of transferring plasmids conferring antibiotic resistance to E. coli clinical isolates on lettuce leaf discs. Furthermore, transformant E. coli from the in planta assay could then colonize the mouse gut microbiome. The target antibiotic resistance plasmid was identified in mouse feces up to 5 days postinfection. We specifically identified in vivo transfer of the plasmid to resident Klebsiella pneumoniae in the mouse gut. Our findings highlight the potential for environmental bacteria exposed to antibiotics to transmit resistance genes to mammalian pathogens during ingestion of leafy greens. IMPORTANCE Previous efforts have correlated antibiotic-fed livestock and meat products with respective antibiotic resistance genes, but virtually no research has been conducted on the transmission of antibiotic resistance from plant foods to the mammalian gut (C. S. Hölzel, J. L. Tetens, and K. Schwaiger, Pathog Dis 15:671–688, 2018, https://doi.org/10.1089/fpd.2018.2501; C. M. Liu et al., mBio 9:e00470-19, 2018, https://doi.org/10.1128/mBio.00470-18; B. Spellberg et al., NAM Perspectives, 2016, https://doi.org/10.31478/201606d; J. O’Neill, Antimicrobials in agriculture and the environment, 2015; Centers for Disease Control and Prevention, Antibiotic resistance threats in the United States, 2019). Here, we sought to determine if horizontal transmission of antibiotic resistance genes can occur between lettuce and the mammalian gut microbiome, using a mouse model. Furthermore, we have created a new model to study horizontal gene transfer on lettuce leaves using an antibiotic-resistant transformant of A. baylyi (AbzeoR).

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Identification of a Novel Conjugative Plasmid in Mycobacteria That Requires Both Type IV and Type VII Secretion

mBio ◽

10.1128/mbio.01744-14 ◽

2014 ◽

Vol 5 (5) ◽

Cited By ~ 39

Author(s):

Roy Ummels ◽

Abdallah M. Abdallah ◽

Vincent Kuiper ◽

Anouar Aâjoud ◽

Marion Sparrius ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Antibiotic Resistance Genes ◽

Conjugative Plasmid ◽

Content Type ◽

Conjugative Plasmids ◽

Type Vii Secretion ◽

Type Iv ◽

Slow Growing

ABSTRACTConjugative plasmids have been identified in a wide variety of different bacteria, ranging from proteobacteria to firmicutes, and conjugation is one of the most efficient routes for horizontal gene transfer. The most widespread mechanism of plasmid conjugation relies on different variants of the type IV secretion pathway. Here, we describe the identification of a novel type of conjugative plasmid that seems to be unique for mycobacteria. Interestingly, while this plasmid is efficiently exchanged between different species of slow-growing mycobacteria, includingMycobacterium tuberculosis, it could not be transferred to any of the fast-growing mycobacteria tested. Genetic analysis of the conjugative plasmid showed the presence of a locus containing homologues of three type IV secretion system components and a relaxase. In addition, a new type VII secretion locus was present. Using transposon insertion mutagenesis, we show that in fact both these secretion systems are essential for conjugation, indicating that this plasmid represents a new class of conjugative plasmids requiring two secretion machineries. This plasmid could form a useful new tool to exchange or introduce DNA in slow-growing mycobacteria.IMPORTANCEConjugative plasmids play an important role in horizontal gene transfer between different bacteria and, as such, in their adaptation and evolution. This effect is most obvious in the spread of antibiotic resistance genes. Thus far, conjugation of natural plasmids has been described only rarely for mycobacterial species. In fact, it is generally accepted thatM. tuberculosisdoes not show any recent sign of horizontal gene transfer. In this study, we describe the identification of a new widespread conjugative plasmid that can also be efficiently transferred toM. tuberculosis. This plasmid therefore poses both a threat and an opportunity. The threat is that, through the acquisition of antibiotic resistance markers, this plasmid could start a rapid spread of antibiotic resistance genes between pathogenic mycobacteria. The opportunity is that we could use this plasmid to generate new tools for the efficient introduction of foreign DNA in slow-growing mycobacteria.

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Role of Horizontal Gene Transfer in the Development of Multidrug Resistance in Haemophilus influenzae

mSphere ◽

10.1128/msphere.00969-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 3

Author(s):

Kristin Hegstad ◽

Haima Mylvaganam ◽

Jessin Janice ◽

Ellen Josefsen ◽

Audun Sivertsen ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Haemophilus Influenzae ◽

Resistance Genes ◽

Mobile Genetic Elements ◽

Beta Lactam ◽

Content Type ◽

Genetic Elements ◽

Wide Range ◽

Chromosomal Genes

ABSTRACT Haemophilus influenzae colonizes the respiratory tract in humans and causes both invasive and noninvasive infections. Resistance to extended-spectrum cephalosporins in H. influenzae is rare in Europe. In this study, we defined acquired resistance gene loci and ftsI mutations in multidrug-resistant (MDR) and/or PBP3-mediated beta-lactam-resistant (rPBP3) H. influenzae strains, intending to understand the mode of spread of antibiotic resistance determinants in this species. Horizontal transfer of mobile genetic elements and transformation with resistance-conferring ftsI alleles were contributory. We found one small plasmid and three novel integrative conjugative elements (ICEs) which carry different combinations of resistance genes. Demonstration of transfer and/or ICE circular forms showed that the ICEs are functional. Two extensively MDR genetically unrelated H. influenzae strains (F and G) from the same geographical region shared an identical novel MDR ICE (Tn6686) harboring blaTEM-1, catA2-like, and tet(B). The first Nordic case of MDR H. influenzae septicemia, strain 0, originating from the same geographical area as these strains, had a similar resistance pattern but contained another ICE [Tn6687 with blaTEM-1, catP and tet(B)] with an overall structure quite similar to that of Tn6686. Comparison of the complete ftsI genes among rPBP3 strains revealed that the entire gene or certain regions of it are identical in genetically unrelated strains, indicating horizontal gene transfer. Our findings illustrate that H. influenzae is capable of acquiring resistance against a wide range of commonly used antibiotics through horizontal gene transfer, in terms of conjugative transfer of ICEs and transformation of chromosomal genes. IMPORTANCE Haemophilus influenzae colonizes the respiratory tract in humans and causes both invasive and noninvasive infections. As a threat to treatment, resistance against critically important antibiotics is on the rise in H. influenzae. Identifying mechanisms for horizontal acquisition of resistance genes is important to understand how multidrug resistance develops. The present study explores the antimicrobial resistance genes and their context in beta-lactam-resistant H. influenzae with coresistance to up to four non-beta-lactam groups. The results reveal that this organism is capable of acquiring resistance to a wide range of commonly used antibiotics through conjugative transfer of mobile genetic elements and transformation of chromosomal genes, resulting in mosaic genes with a broader resistance spectrum. Strains with chromosomally mediated resistance to extended-spectrum cephalosporins, co-trimoxazole, and quinolones combined with mobile genetic elements carrying genes mediating resistance to ampicillin, tetracyclines, and chloramphenicol have been reported, and further dissemination of such strains represents a particular concern.

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ARB and ARGs survived from the extremely acidity posing a risk on intestinal bacteria in an in vitro digestion model by horizontal gene transfer

10.21203/rs.3.rs-392269/v1 ◽

2021 ◽

Author(s):

Qiujie Cai ◽

Yanbin Xu ◽

Min Zhou ◽

Ling Yu ◽

Pengqian Ouyang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

16S Rrna ◽

Gastric Juice ◽

Total Population ◽

Intestinal Bacteria ◽

In Vitro Digestion ◽

Transfer Potential

Abstract Background: Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) have been considered as emerging contaminants, which even might be closely related to human health.Methods: To investigate the disease-producing risk of ARB and the horizontal gene transfer (HGT) risks of both extracellular ARGs (eARGs) and intracellular ARGs (iARGs), an in vitro digestion model was established to simulate the process of ARB and ARGs going through digestive tract. CTC/DAPI-FCM assay was used to study the survival of ARB during digestion, and the changes of genes (including tetA, tetG, tetM, sul1, sul2, bla EBC, bla FOX, intI1 and 16S rRNA) were determined by QPCR.Results: The results showed that ARB were mostly affected by pH of gastric juice. About 99% ARB (total population of 2.45 × 109–2.54 × 109) were killed by the gastric juice of pH 2.0 for the severely damage of bacterial cell membrane, but more than 80% ARB (total population of 2.71 × 109–3.90 × 109) were still alive with intact cell membrane when the pH of gastric juice increased to 3.0 and above. ARGs, intI1 and 16S rRNA could be detectable even at extreme pH when most bacteria died. The eARGs (accounting for 0.03%–24.56% of total genes) were less than iARGs obviously. The eARGs showed greater HGT potential than that of iARGs, suggesting transformation occurs more easily than conjugation. The transfer potential followed the order as: tet (100%) > sul (75%) > bla (58%), related to the high correlation of intI1 with tetA and sul2 (p < 0.01). Moreover, gastric juice of pH 1.0 could decrease the transfer frequency of ARGs by 2–3 order of magnitude compared to the control, but still threatening human health.Conclusions: Under the treatment of digestive juice, ARGs still have high gene horizontal transfer potential, suggesting that food-borne ARB pose a risk of ARGs horizontal transfer to intestinal bacteria.

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Prophage-Mediated Disruption of Genetic Competence in Staphylococcus pseudintermedius

mSystems ◽

10.1128/msystems.00684-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 5

Author(s):

Michael R. Brooks ◽

Lyan Padilla-Vélez ◽

Tarannum A. Khan ◽

Azaan A. Qureshi ◽

Jason B. Pieper ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

North America ◽

Horizontal Gene Transfer ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Fluoroquinolone Resistance ◽

Genetic Competence ◽

Staphylococcus Pseudintermedius ◽

Content Type

ABSTRACT Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a major cause of soft tissue infections in dogs and occasionally infects humans. Hypervirulent multidrug-resistant (MDR) MRSP clones have emerged globally. The sequence types ST71 and ST68, the major epidemic clones of Europe and North America, respectively, have spread to other regions. The genetic factors underlying the success of these clones have not been investigated thoroughly. Here, we performed a comprehensive genomic analysis of 371 S. pseudintermedius isolates to dissect the differences between major clonal lineages. We show that the prevalence of genes associated with antibiotic resistance, virulence, prophages, restriction-modification (RM), and CRISPR/Cas systems differs significantly among MRSP clones. The isolates with GyrA+GrlA mutations, conferring fluoroquinolone resistance, carry more of these genes than those without GyrA+GrlA mutations. ST71 and ST68 clones carry lineage-specific prophages with genes that are likely associated with their increased fitness and virulence. We have discovered that a prophage, SpST71A, is inserted within the comGA gene of the late competence operon comG in the ST71 lineage. A functional comG is essential for natural genetic competence, which is one of the major modes of horizontal gene transfer (HGT) in bacteria. The RM and CRISPR/Cas systems, both major genetic barriers to HGT, are also lineage specific. Clones harboring CRISPR/Cas or a prophage-disrupted comG exhibited less genetic diversity and lower rates of recombination than clones lacking these systems. After Listeria monocytogenes, this is the second example of prophage-mediated competence disruption reported in any bacteria. These findings are important for understanding the evolution and clonal expansion of MDR MRSP clones. IMPORTANCE Staphylococcus pseudintermedius is a bacterium responsible for clinically important infections in dogs and can infect humans. In this study, we performed genomic analysis of 371 S. pseudintermedius isolates to understand the evolution of antibiotic resistance and virulence in this organism. The analysis covered significant reported clones, including ST71 and ST68, the major epidemic clones of Europe and North America, respectively. We show that the prevalence of genes associated with antibiotic resistance, virulence, prophages, and horizontal gene transfer differs among clones. ST71 and ST68 carry prophages with novel virulence and antibiotic resistance genes. Importantly, site-specific integration of a prophage, SpST71A, has led to the disruption of the genetic competence operon comG in ST71 clone. A functional comG is essential for the natural uptake of foreign DNA and thus plays an important role in the evolution of bacteria. This study provides insight into the emergence and evolution of antibiotic resistance and virulence in S. pseudintermedius, which may help in efforts to combat this pathogen.

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Fluorescence-Based Detection of Natural Transformation in Drug-ResistantAcinetobacter baumannii

Journal of Bacteriology ◽

10.1128/jb.00181-18 ◽

2018 ◽

Vol 200 (19) ◽

Cited By ~ 11

Author(s):

Anne-Sophie Godeux ◽

Agnese Lupo ◽

Marisa Haenni ◽

Simon Guette-Marquet ◽

Gottfried Wilharm ◽

...

Keyword(s):

Flow Cytometry ◽

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Natural Transformation ◽

Multidrug Resistant ◽

New Method ◽

Content Type ◽

Transfer Mechanisms ◽

Multiple Antibiotics

ABSTRACTAcinetobacter baumanniiis a nosocomial agent with a high propensity for developing resistance to antibiotics. This ability relies on horizontal gene transfer mechanisms occurring in theAcinetobactergenus, including natural transformation. To study natural transformation in bacteria, the most prevalent method uses selection for the acquisition of an antibiotic resistance marker in a target chromosomal locus by the recipient cell. Most clinical isolates ofA. baumanniiare resistant to multiple antibiotics, limiting the use of such selection-based methods. Here, we report the development of a phenotypic and selection-free method based on flow cytometry to detect transformation events in multidrug-resistant (MDR) clinicalA. baumanniiisolates. To this end, we engineered a translational fusion between the abundant and conservedA. baumanniinucleoprotein (HU) and the superfolder green fluorescent protein (sfGFP). The new method was benchmarked against the conventional antibiotic selection-based method. Using this new method, we investigated several parameters affecting transformation efficiencies and identified conditions of transformability one hundred times higher than those previously reported. Using optimized transformation conditions, we probed natural transformation in a set of MDR clinical and nonclinical animalA. baumanniiisolates. Regardless of their origin, the majority of the isolates displayed natural transformability, indicative of a conserved trait in the species. Overall, this new method and optimized protocol will greatly facilitate the study of natural transformation in the opportunistic pathogenA. baumannii.IMPORTANCEAntibiotic resistance is a pressing global health concern with the rise of multiple and panresistant pathogens. The rapid and unfailing resistance to multiple antibiotics of the nosocomial agentAcinetobacter baumannii, notably to carbapenems, prompt to understand the mechanisms behind acquisition of new antibiotic resistance genes. Natural transformation, one of the horizontal gene transfer mechanisms in bacteria, was only recently described inA. baumanniiand could explain its ability to acquire resistance genes. We developed a reliable method to probe and study natural transformation mechanism inA. baumannii. More broadly, this new method based on flow cytometry will allow experimental detection and quantification of horizontal gene transfer events in multidrug-resistantA. baumannii.

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Mouse Genetic Background Affects Transfer of an Antibiotic Resistance Plasmid in the Gastrointestinal Tract

mSphere ◽

10.1128/msphere.00847-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 2

Author(s):

Logan C. Ott ◽

Zachary R. Stromberg ◽

Graham A. J. Redweik ◽

Michael J. Wannemuehler ◽

Melha Mellata

Keyword(s):

Antibiotic Resistance ◽

Gastrointestinal Tract ◽

Plasmid Transfer ◽

Host Factors ◽

Mouse Strains ◽

Wild Type ◽

Content Type ◽

E Coli ◽

Mouse Genetic

ABSTRACT Dissemination of antibiotic resistance (AR) genes, often on plasmids, leads to antibiotic-resistant bacterial infections, which is a major problem for animal and public health. Bacterial conjugation is the primary route of AR gene transfer in the mammalian gastrointestinal tract. Significant gaps in knowledge about which gastrointestinal communities and host factors promote plasmid transfer remain. Here, we used Salmonella enterica serovar Kentucky strain CVM29188 carrying plasmid pCVM29188_146 (harboring streptomycin and tetracycline resistance genes) to assess plasmid transfer to Escherichia coli under in vitro conditions and in various mouse strains with a conventional or defined microbiota. As an initial test, the transfer of pCVM29188_146 to the E. coli strains was confirmed in vitro. Colonization resistance and, therefore, a lack of plasmid transfer were found in wild-type mice harboring a conventional microbiota. Thus, mice harboring the altered Schaedler flora (ASF), or ASF mice, were used to probe for host factors in the context of a defined microbiota. To assess the influence of inflammation on plasmid transfer, we compared interleukin-10 gene-deficient 129S6/SvEv ASF mice (proinflammatory environment) to wild-type 129S6/SvEv ASF mice and found no difference in transconjugant yields. In contrast, the mouse strain influenced plasmid transfer, as C3H/HeN ASF mice had significantly lower levels of transconjugants than 129S6/SvEv ASF mice. Although gastrointestinal members were identical between the ASF mouse strains, a few differences from C3H/HeN ASF mice were detected, with C3H/HeN ASF mice having significantly lower abundances of ASF members 356 (Clostridium sp.), 492 (Eubacterium plexicaudatum), and 502 (Clostridium sp.) than 129S6/SvEv ASF mice. Overall, we demonstrate that microbiota complexity and mouse genetic background influence in vivo plasmid transfer. IMPORTANCE Antibiotic resistance is a threat to public health. Many clinically relevant antibiotic resistance genes are carried on plasmids that can be transferred to other bacterial members in the gastrointestinal tract. The current study used a murine model to study the transfer of a large antibiotic resistance plasmid from a foodborne Salmonella strain to a gut commensal E. coli strain in the gastrointestinal tract. We found that different mouse genetic backgrounds and a different diversity of microbial communities influenced the level of Escherichia coli that acquired the plasmid in the gastrointestinal tract. This study suggests that the complexity of the microbial community and host genetics influence plasmid transfer from donor to recipient bacteria.

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TheblpLocus of Streptococcus pneumoniae Plays a Limited Role in the Selection of Strains That Can Cocolonize the Human Nasopharynx

Applied and Environmental Microbiology ◽

10.1128/aem.01048-16 ◽

2016 ◽

Vol 82 (17) ◽

pp. 5206-5215 ◽

Cited By ~ 5

Author(s):

Carina Valente ◽

Suzanne Dawid ◽

Francisco R. Pinto ◽

Jason Hinds ◽

Alexandra S. Simões ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Experimental Models ◽

Nasopharyngeal Colonization ◽

Content Type ◽

Limited Role ◽

Multiple Strains ◽

The Impact

ABSTRACTNasopharyngeal colonization is important forStreptococcus pneumoniaeevolution, providing the opportunity for horizontal gene transfer when multiple strains co-occur. Although colonization with more than one strain of pneumococcus is common, the factors that influence the ability of strains to coexist are not known. A highly variableblp(bacteriocin-like peptide) locus has been identified in all sequenced strains ofS. pneumoniae. This locus controls the regulation and secretion of bacteriocins, small peptides that target other bacteria. In this study, we analyzed a series of cocolonizing isolates to evaluate the impact of theblplocus on human colonization to determine whether competitive phenotypes of bacteriocin secretion restrict cocolonization. We identified a collection of 135 nasopharyngeal samples cocolonized with two or more strains, totaling 285 isolates. Theblplocus of all strains was characterized genetically with regard to pheromone type, bacteriocin/immunity content, and potential for locus functionality. Inhibitory phenotypes of bacteriocin secretion and locus activity were assessed through overlay assays. Isolates from single colonizations (n= 298) were characterized for comparison. Cocolonizing strains had a high diversity ofblpcassettes; approximately one-third displayed an inhibitory phenotypein vitro. Despitein vitroevidence of competition, pneumococci cocolonized the subjects independently ofblppheromone type (P= 0.577), bacteriocin/immunity content,blplocus activity (P= 0.798), and inhibitory phenotype (P= 0.716). In addition, no significant differences were observed when single and cocolonizing strains were compared. Despite clear evidence ofblp-mediated competition in experimental models, the results of our study suggest that theblplocus plays a limited role in restricting pneumococcal cocolonization in humans.IMPORTANCENasopharyngeal colonization withStreptococcus pneumoniae(pneumococcus) is important for pneumococcal evolution, as the nasopharynx represents the major site for horizontal gene transfer when multiple strains co-occur, a phenomenon known as cocolonization. Understanding how pneumococcal strains interact within the competitive environment of the nasopharynx is of chief importance in the context of pneumococcal ecology. In this study, we used an unbiased collection of naturally co-occurring pneumococcal strains and showed that a biological process frequently used by bacteria for competition—bacteriocin production—is not decisive in the coexistence of pneumococci in the host, in contrast to what has been shown in experimental models.

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CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens

10.1101/2021.04.12.439454 ◽

2021 ◽

Author(s):

Elizabeth Pursey ◽

Tatiana Dimitriu ◽

Fernanda L. Paganelli ◽

Edze R. Westra ◽

Stineke van Houte

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Resistance Genes ◽

Bacterial Pathogens ◽

Genetic Material ◽

Antibiotic Resistance Genes ◽

Mobile Genetic Elements ◽

Genetic Elements ◽

Defence System

AbstractThe acquisition of antibiotic resistance genes via horizontal gene transfer is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of antibiotic resistance. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of antibiotic resistance. We analysed ~40,000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens including Enterococcus, Staphylococcus, Acinetobacter and Pseudomonas. We modelled the association between CRISPR-Cas and indicators of horizontal gene transfer, and found that pathogens with a CRISPR-Cas system were less likely to carry antibiotic resistance genes than those lacking this defence system. Analysis of the mobile genetic elements targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of antibiotic resistance. These results suggest a potential “immunocompromised” state for multidrug-resistant strains that may be exploited in tailored interventions that rely on mobile genetic elements, such as phage or phagemids, to treat infections caused by bacterial pathogens.

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