Experimental support for multidrug resistance transfer potential in the preterm infant gut microbiota

The preterm infant gut microbiota is influenced by environmental, endogenous, maternal, and genetic factors. Although siblings share similar gut microbial composition, it is not known how genetic relatedness affects alpha diversity and specific taxa abundances in preterm infants. We analyzed the 16S rRNA gene content of stool samples, ≤ and >3 weeks postnatal age, and clinical data from preterm multiplets and singletons at two Neonatal Intensive Care Units (NICUs), Tampa General Hospital (TGH; FL, USA) and Carle Hospital (IL, USA). Weeks on bovine milk-based fortifier (BMF) and weight gain velocity were significant predictors of alpha diversity. Alpha diversity between siblings were significantly correlated, particularly at ≤3 weeks postnatal age and in the TGH NICU, after controlling for clinical factors. Siblings shared higher gut microbial composition similarity compared to unrelated individuals. After residualizing against clinical covariates, 30 common operational taxonomic units were correlated between siblings across time points. These belonged to the bacterial classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Erysipelotrichia, and Negativicutes. Besides the influence of BMF and weight variables on the gut microbial diversity, our study identified gut microbial similarities between siblings that suggest genetic or shared maternal and environmental effects on the preterm infant gut microbiota.

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Persistence of Suspected Probiotic Organisms in Preterm Infant Gut Microbiota Weeks After Probiotic Supplementation in the NICU

Frontiers in Microbiology ◽

10.3389/fmicb.2020.574137 ◽

2020 ◽

Vol 11 ◽

Author(s):

Efrah I. Yousuf ◽

Marilia Carvalho ◽

Sara E. Dizzell ◽

Stephanie Kim ◽

Elizabeth Gunn ◽

...

Keyword(s):

Gut Microbiota ◽

Preterm Infant ◽

Probiotic Supplementation

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Preterm infant gut microbiota affects intestinal epithelial development in a humanized microbiome gnotobiotic mouse model

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00022.2016 ◽

2016 ◽

Vol 311 (3) ◽

pp. G521-G532 ◽

Cited By ~ 29

Author(s):

Yueyue Yu ◽

Lei Lu ◽

Jun Sun ◽

Elaine O. Petrof ◽

Erika C. Claud

Keyword(s):

Weight Gain ◽

Mouse Model ◽

Gut Microbiota ◽

Preterm Infant ◽

Microbial Communities ◽

Goblet Cells ◽

Paneth Cells ◽

Stem Cell Marker ◽

Intestinal Development ◽

The Impact

Development of the infant small intestine is influenced by bacterial colonization. To promote establishment of optimal microbial communities in preterm infants, knowledge of the beneficial functions of the early gut microbiota on intestinal development is needed. The purpose of this study was to investigate the impact of early preterm infant microbiota on host gut development using a gnotobiotic mouse model. Histological assessment of intestinal development was performed. The differentiation of four epithelial cell lineages (enterocytes, goblet cells, Paneth cells, enteroendocrine cells) and tight junction (TJ) formation was examined. Using weight gain as a surrogate marker for health, we found that early microbiota from a preterm infant with normal weight gain (MPI-H) induced increased villus height and crypt depth, increased cell proliferation, increased numbers of goblet cells and Paneth cells, and enhanced TJs compared with the changes induced by early microbiota from a poor weight gain preterm infant (MPI-L). Laser capture microdissection (LCM) plus qRT-PCR further revealed, in MPI-H mice, a higher expression of stem cell marker Lgr5 and Paneth cell markers Lyz1 and Cryptdin5 in crypt populations, along with higher expression of the goblet cell and mature enterocyte marker Muc3 in villus populations. In contrast, MPI-L microbiota failed to induce the aforementioned changes and presented intestinal characteristics comparable to a germ-free host. Our data demonstrate that microbial communities have differential effects on intestinal development. Future studies to identify pioneer settlers in neonatal microbial communities necessary to induce maturation may provide new insights for preterm infant microbial ecosystem therapeutics.

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Horizontal Transfer of the Salmonella enterica Serovar Infantis Resistance and Virulence Plasmid pESI to the Gut Microbiota of Warm-Blooded Hosts

mBio ◽

10.1128/mbio.01395-16 ◽

2016 ◽

Vol 7 (5) ◽

Cited By ~ 35

Author(s):

Gili Aviv ◽

Galia Rahav ◽

Ohad Gal-Mor

Keyword(s):

Multidrug Resistance ◽

Gut Microbiota ◽

Salmonella Enterica ◽

Pathogenic Bacteria ◽

Lactobacillus Reuteri ◽

Bacterial Species ◽

Microbial Evolution ◽

Virulence Plasmid ◽

Transmission Properties

ABSTRACT Salmonella enterica serovar Infantis is one of the prevalent salmonellae worldwide. Recently, we showed that the emergence of S . Infantis in Israel was facilitated by the acquisition of a unique megaplasmid (pESI) conferring multidrug resistance and increased virulence phenotypes. Here we elucidate the ecology, transmission properties, and regulation of pESI. We show that despite its large size (~280 kb), pESI does not impose a significant metabolic burden in vitro and that it has been recently fixed in the domestic S . Infantis population. pESI conjugation and the transcription of its pilus ( pil ) genes are inhibited at the ambient temperature (27°C) and by ≥1% bile but increased under temperatures of 37 to 41°C, oxidative stress, moderate osmolarity, and the microaerobic conditions characterizing the intestinal environment of warm-blooded animals. The pESI-encoded protein TraB and the oxygen homeostasis regulator Fnr were identified as transcriptional regulators of pESI conjugation. Using the mouse model, we show that following S . Infantis infection, pESI can be horizontally transferred to the gut microbiota, including to commensal Escherichia coli strains. Possible transfer, but not persistence, of pESI was also observed into Gram-positive mouse microbiota species, especially Lactobacillus reuteri . Moreover, pESI was demonstrated to further disseminate from gut microbiota to S. enterica serovar Typhimurium, in the context of gastrointestinal infection. These findings exhibit the ability of a selfish clinically relevant megaplasmid to distribute to and from the microbiota and suggest an overlooked role of the microbiota as a reservoir of mobile genetic elements and intermediator in the spread of resistance and virulence genes between commensals and pathogenic bacteria. IMPORTANCE Plasmid conjugation plays a key role in microbial evolution, enabling the acquisition of new phenotypes, including resistance and virulence. Salmonella enterica serovar Infantis is one of the ubiquitous salmonellae worldwide and a major cause of foodborne infections. Previously, we showed that the emergence of S . Infantis in Israel has involved the acquisition of a unique megaplasmid (pESI) conferring multidrug resistance and increased virulence phenotypes. Recently, the emergence of another S . Infantis strain carrying a pESI-like plasmid was identified in Italy, suggesting that the acquisition of pESI may be common to different emergent S . Infantis populations globally. Transmission of this plasmid to other strains or bacterial species is an alarming scenario. Understanding the ecology, regulation, and transmission properties of clinically relevant plasmids and the role of the microbiota in their spreading offers a new mechanism explaining the emergence of new pathogenic and resistant biotypes and may assist in the development of appropriate surveillance and prevention measures.

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Detection and characterization of verotoxin-producing strains among sorbitol non-fermenting Escherichia coli

Eastern Mediterranean Health Journal ◽

10.26719/2001.7.4-5.756 ◽

2001 ◽

Vol 7 (4-5) ◽

pp. 756-762

Author(s):

A. Jafari ◽

M. Katouli ◽

F. Shokouhi ◽

S. Bouzari

Keyword(s):

Escherichia Coli ◽

Polymerase Chain Reaction ◽

Antibiotic Resistance ◽

Multidrug Resistance ◽

High Rate ◽

Cell Adherence ◽

Chain Reaction ◽

Resistance Transfer ◽

Polymerase Chain

The presence of genes for verotoxin 1 and 2 [VT1 and 2] among sorbitol non-fermenting Escherichia coli isolates from diarrhoeal cases was assessed using polymerase chain reaction assay. Of 60 [88%] positive isolates, 37 [62%] harboured VT1 and 23 [38%] both VT1 and VT2. In HeLa cell adherence assay, 48 [71%] isolates exhibited mannose-resistant adherence to HeLa cells. Multidrug resistance was observed in 56 [82%] isolates, with ampicillin, chloramphenicol, streptomycin, sulfamethoxazole-trimethoprim and tetracycline pattern being the most common. There were 13 common and 22 single biochemical phenotypes identified. Isolates belonging to common biochemical phenotypes normally had a similar pattern of adherence and VT production, but differed greatly in their pattern of antibiotic resistance, pointing to a high rate of antibiotic-resistance transfer among these isolates.

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Alleviation of Cholesterol Gallstones by Lactobacillus Targeting the Gut Microbiota Depends on Global Farnesoid X Receptor-Mediated Bile Acid Metabolism

10.21203/rs.3.rs-120683/v1 ◽

2020 ◽

Author(s):

Xinjian Wan ◽

Xin Ye ◽

Qian Zhuang ◽

Zhixia Dong ◽

Xiaoxin Wang ◽

...

Keyword(s):

Multidrug Resistance ◽

Bile Acid ◽

Gut Microbiota ◽

Lactobacillus Reuteri ◽

Cholesterol Gallstone ◽

Farnesoid X Receptor ◽

Bile Acid Metabolism ◽

Protective Effects ◽

Lithogenic Diet ◽

Cytochrome P450 Family

Abstract Background Cholesterol gallstone (CGS) disease is characterized by an imbalance in bile acid (BA) metabolism and is closely associated with gut microbiota disorders. However, the role and mechanism by which probiotics targeting the gut microbiota attenuate CGS are still unknown. In this study, Lactobacillus reuteri CGMCC 17942 (LR) and L. plantarum CGMCC 14407 (LP) were individually administered to lithogenic diet (LD)-fed mice at a dosage of 109 CFU/day for 8 weeks. Results Both Lactobacillus strains significantly reduced LD-induced gallstones, hepatic steatosis, and hyperlipidemia. These strains modulated serum BA profiles, with significantly decreased conjugated primary BA taurine-β-muricholic acid (T-β-MCA), an FXR antagonist. At the molecular level, LR and LP increased Farnesoid X Receptor (FXR) expression in the liver but not in the ileum, increased the levels of ileum and liver fibroblast growth factor 15 (FGF15) and liver FGFR4, small heterodimer partner (SHP), and subsequently reduced cholesterol 7α-hydroxylase (CYP7A1) and cytochrome P450 family 7 subfamily B polypeptide 1 (CYP7B1) to inhibit BA synthesis in the liver. At the same time, the two strains enhanced BA transport by increasing the levels of multidrug-resistance-associated protein homologs (MRP) 3/4, multidrug-resistance-associated protein homologs (MRP) 3/4, hepatic multidrug resistance protein (MDR2) and bile salt export pump (BSEP) mRNA in the liver. In addition, both LR and LP reduced LD-associated gut microbiota dysbiosis. LR increased the relative abundance of Muribaculaceae, while LP increased that of Akkermansia. The changed gut microbiota was significantly negatively correlated with the grade and incidence of gallstones, hyperlipidemia, the level of T-β-MCA in serum, or the gene expression levels of Fxr in liver. Furthermore, the protective effects of the two strains were abolished by a global but not intestinal-specific FXR antagonist. Conclusions Taken together, our results suggested that Lactobacillus might relieve gallstones through FXR-dependent regulation of BA synthesis and transport.

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Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life

Microbiome ◽

10.1186/s40168-017-0290-6 ◽

2017 ◽

Vol 5 (1) ◽

Cited By ~ 16

Author(s):

Weili Xiong ◽

Christopher T. Brown ◽

Michael J. Morowitz ◽

Jillian F. Banfield ◽

Robert L. Hettich

Keyword(s):

Gut Microbiota ◽

Preterm Infant ◽

Early Life ◽

Species Specific

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Bioinformatics analysis of antimicrobial resistance genes and prophages colocalized in human gut metagenomes

Biomeditsinskaya Khimiya ◽

10.18097/pbmc20176306508 ◽

2017 ◽

Vol 63 (6) ◽

pp. 508-512 ◽

Cited By ~ 1

Author(s):

E.V. Starikova ◽

N.A. Prianichnikov ◽

E. Zdobnov ◽

V.M. Govorun

Keyword(s):

Multidrug Resistance ◽

Gut Microbiota ◽

Resistance Genes ◽

Bioinformatics Analysis ◽

Symbiotic Bacteria ◽

Antibiotics Resistance ◽

Human Gut ◽

Antibiotic Resistant ◽

Antimicrobial Resistance Genes ◽

Resistant Strains

The constant increase of antibiotic-resistant strains of bacteria is caused by extensive uses of antibiotics in medicine and animal breeding. It was suggested that the gut microbiota serves as a reservoir for antibiotics resistance genes that can be carried from symbiotic bacteria to pathogenic ones, in particular, as a result of transduction. In the current study, we have searched for antibiotics resistance genes that are located inside prophages in human gut microbiota using PHASTER prophage predicting tool and CARD antibiotics resistance database. After analysing metagenomic assemblies of eight samples of antibiotic treated patients, lsaE, mdfA and cpxR/cpxA genes were identified inside prophages. The abovementioned genes confer resistance to antimicrobial peptides, pleuromutilin, lincomycins, streptogramins and multidrug resistance. Three (0.46%) of 659 putative prophages predicted in metagenomic assemblies contained antibiotics resistance genes in their sequences.

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Evolution of Intestinal Gases and Fecal Short-Chain Fatty Acids Produced in vitro by Preterm Infant Gut Microbiota During the First 4 Weeks of Life

Frontiers in Pediatrics ◽

10.3389/fped.2021.726193 ◽

2021 ◽

Vol 9 ◽

Author(s):

Xuefang Wang ◽

Juan Li ◽

Na Li ◽

Kunyu Guan ◽

Di Yin ◽

...

Keyword(s):

Fatty Acids ◽

Acetic Acid ◽

Gut Microbiota ◽

Preterm Infant ◽

Preterm Infants ◽

Short Chain Fatty Acids ◽

Short Chain ◽

Delivery Mode ◽

Chain Fatty Acids

Background: The production of intestinal gases and fecal short-chain fatty acids (SCFAs) by infant gut microbiota may have a significant impact on their health, but information about the composition and volume of intestinal gases and SCFA profiles in preterm infants is scarce.Objective: This study examined the change of the composition and volume of intestinal gases and SCFA profiles produced by preterm infant gut microbiota in vitro during the first 4 weeks of life.Methods: Fecal samples were obtained at five time points (within 3 days, 1 week, 2 weeks, 3 weeks, and 4 weeks) from 19 preterm infants hospitalized in the neonatal intensive care unit (NICU) of Shanghai Children's Hospital, Shanghai Jiao Tong University between May and July 2020. These samples were initially inoculated into four different media containing lactose (LAT), fructooligosaccharide (FOS), 2′-fucosyllactose (FL-2), and galactooligosaccharide (GOS) and thereafter fermented for 24 h under conditions mimicking those of the large intestine at 37.8°C under anaerobic conditions. The volume of total intestinal gases and the concentrations of individual carbon dioxide (CO2), hydrogen (H2), methane (CH4), and hydrogen sulfide (H2S) were measured by a gas analyzer. The concentrations of total SCFAs, individual acetic acid, propanoic acid, butyric acid, isobutyric acid, pentanoic acid, and valeric acid were measured by gas chromatography (GC).Results: The total volume of intestinal gases (ranging from 0.01 to 1.64 ml in medium with LAT; 0–1.42 ml with GOS; 0–0.91 ml with FOS; and 0–0.44 ml with FL-2) and the concentrations of CO2, H2, H2S, and all six fecal SCFAs increased with age (p-trends < 0.05). Among them, CO2 was usually the predominant intestinal gas, and acetic acid was usually the predominant SCFA. When stratified by birth weight (<1,500 and ≥1,500 g), gender, and delivery mode, the concentration of CO2 was more pronounced among infants whose weight was ≥1,500 g than among those whose weight was <1,500 g (p-trends < 0.05).Conclusions: Our findings suggested that the intestinal gases and SCFAs produced by preterm infant gut microbiota in vitro increased with age during the first 4 weeks of life.

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