Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema

Abstract Background While there is increasing knowledge about the gut microbiome, the factors influencing and the significance of the gut resistome are still not well understood. Infant gut commensals risk transferring multidrug-resistant antibiotic resistance genes (ARGs) to pathogenic bacteria. The rapid spread of multidrug-resistant pathogenic bacteria is a worldwide public health concern. Better understanding the naïve infant gut resistome may build the evidence base for antimicrobial stewardship in both humans and in the food industry. Given the high carriage rate of extended spectrum beta-lactamase (ESBL)- producing Enterobacteriaceae in Asia, we aimed to evaluate community prevalence, dynamics, and longitudinal changes in antibiotic resistance gene (ARG) profiles and prevalence of ESBL-producing .E coli and K. pneumoniae in the intestinal microbiome of infants participating in the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) study, a longitudinal cohort study of pregnant women and their infants. Methods We analysed ARGs in the first year of life among 75 infants who had stool samples collected at multiple timepoints using metagenomics. Results The mean number of ARGs per infant increased with age. The most common ARGs identified confer resistance to aminoglycoside, beta-lactam, macrolide and tetracycline antibiotics; all infants harboured these antibiotic resistance genes at some point in the first year of life. Few ARGs persisted throughout the first year of life. Beta-lactam resistant Escherichia coli and Klebsiella pneumoniae were detected in 4 (5.3%) and 32 (42.7%) of subjects respectively. Conclusion In this longitudinal cohort study of infants living in a region with high endemic antibacterial resistance, we demonstrate that the majority of the infants harboured several antibiotic resistance genes in their gut and showed that the infant gut resistome is diverse and dynamic over the first year of life.

Download Full-text

Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema

10.21203/rs.2.18486/v3 ◽

2020 ◽

Author(s):

Evelyn Loo(Former Corresponding Author) ◽

Amanda Zain ◽

Gaik Chin Yap ◽

Rikky W Purbojati ◽

Daniela I Drautz-Moses ◽

...

Keyword(s):

Antibiotic Resistance ◽

Cohort Study ◽

Resistance Genes ◽

Pathogenic Bacteria ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

First Year ◽

Beta Lactam ◽

First Year Of Life

Abstract Background While there is increasing knowledge about the gut microbiome, the factors influencing and the significance of the gut resistome are still not well understood. Infant gut commensals risk transferring multidrug-resistant antibiotic resistance genes (ARGs) to pathogenic bacteria. The rapid spread of multidrug-resistant pathogenic bacteria is a worldwide public health concern. Better understanding the naïve infant gut resistome may build the evidence base for antimicrobial stewardship in both humans and in the food industry. Given the high carriage rate of extended spectrum beta-lactamase (ESBL)- producing Enterobacteriaceae in Asia, we aimed to evaluate community prevalence, dynamics, and longitudinal changes in antibiotic resistance gene (ARG) profiles and prevalence of ESBL-producing E. coli and K. pneumoniae in the intestinal microbiome of infants participating in the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) study, a longitudinal cohort study of pregnant women and their infants. Methods: We analysed ARGs in the first year of life among 75 infants at risk of eczema who had stool samples collected at multiple timepoints using metagenomics. Results: The mean number of ARGs per infant increased with age. The most common ARGs identified confer resistance to aminoglycoside, beta-lactam, macrolide and tetracycline antibiotics; all infants harboured these antibiotic resistance genes at some point in the first year of life. Few ARGs persisted throughout the first year of life. Beta-lactam resistant Escherichia coli and Klebsiella pneumoniae were detected in 4 (5.3%) and 32 (42.7%) of subjects respectively. Conclusion: In this longitudinal cohort study of infants living in a region with high endemic antibacterial resistance, we demonstrate that majority of the infants harboured several antibiotic resistance genes in their gut and showed that the infant gut resistome is diverse and dynamic over the first year of life.

Download Full-text

Longitudinal assessment of antibiotic resistance gene profiles from the infant gut microbiome

10.21203/rs.2.18486/v1 ◽

2019 ◽

Author(s):

Evelyn Loo ◽

Amanda Zain ◽

Gaik Chin Yap ◽

Rikky W Purbojati ◽

Daniela I Drautz-Moses ◽

...

Keyword(s):

Antibiotic Resistance ◽

Cohort Study ◽

Resistance Gene ◽

Resistance Genes ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Longitudinal Cohort Study ◽

First Year ◽

Beta Lactam ◽

First Year Of Life

Abstract Background: The rapid spread of multidrug- resistant pathogenic bacteria is a worldwide public health concern. Given the high carriage rate of extended spectrum beta-lactamase (ESBL)- producing Enterobacteriaceae in Asia, we aimed to evaluate community prevalence and dynamics by studying the longitudinal changes in antibiotic resistance gene (ARG) profiles and prevalence of ESBL-producing E coli and K. pneumoniae in the intestinal microbiome of infants participating in the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) study, a longitudinal cohort study of pregnant women and their infants. Methods: We analysed the antibiotic resistance genes profile in the first year of life among 75 infants who had stool samples collected at multiple timepoints using metagenomics. Results: The mean number of ARGs per infant increased with age. The most common ARGs identified confer resistance to aminoglycoside, beta-lactam, macrolide and tetracycline antibiotics; all infants harboured these antibiotic resistance genes at some point in the first year of life. Few ARGs persisted throughout the first year of life. Beta-lactam resistant Escherichia coli and Klebsiella pneumoniae were detected in 4 (5.3%) and 32 (42.7%) of subjects respectively. Conclusion: In this longitudinal cohort study of healthy infants living in a region with high endemic antibacterial resistance, we demonstrate that majority of the infants harboured a number of antibiotic resistance genes in their gut and showed that the infant gut resistome is diverse and dynamic over the first year of life.

Download Full-text

Antimicrobial Resistance and CRISPR Typing Among Salmonella Isolates From Poultry Farms in China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.730046 ◽

2021 ◽

Vol 12 ◽

Author(s):

Cui Li ◽

Yulong Wang ◽

Yufeng Gao ◽

Chao Li ◽

Boheng Ma ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Direct Repeat ◽

Epidemiological Data ◽

Multidrug Resistant ◽

Typing Method ◽

Crispr Locus ◽

Research Areas

Although knowledge of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system has been applied in many research areas, comprehensive studies of this system in Salmonella, particularly in analysis of antibiotic resistance, have not been reported. In this work, 75 Salmonella isolates obtained from broilers or broilers products were characterized to determine their antimicrobial susceptibilities, antibiotic resistance gene profiles, and CRISPR array diversities, and genotyping was explored. In total, 80.00% (60/75) of the strains were multidrug resistant, and the main pattern observed in the isolates was CN-AZM-AMP-AMC-CAZ-CIP-ATM-TE-SXT-FOS-C. The resistance genes of streptomycin (aadA), phenicol (floR-like and catB3-like), β-lactams (blaTEM, blaOXA, and blaCTX), tetracycline [tet(A)-like], and sulfonamides (sul1 and sul2) appeared at higher frequencies among the corresponding resistant isolates. Subsequently, we analyzed the CRISPR arrays and found 517 unique spacer sequences and 31 unique direct repeat sequences. Based on the CRISPR spacer sequences, we developed a novel typing method, CRISPR locus three spacer sequences typing (CLTSST), to help identify sources of Salmonella outbreaks especially correlated with epidemiological data. Compared with multi-locus sequence typing (MLST), conventional CRISPR typing (CCT), and CRISPR locus spacer pair typing (CLSPT), discrimination using CLTSST was weaker than that using CCT but stronger than that using MLST and CLSPT. In addition, we also found that there were no close correlations between CRISPR loci and antibiotics but had close correlations between CRISPR loci and antibiotic resistance genes in Salmonella isolates.

Download Full-text

Monitoring and Evaluation of Antibiotic Resistance Genes in Three Rivers in Northeast China

10.21203/rs.3.rs-313046/v2 ◽

2021 ◽

Author(s):

Chen Zhao ◽

Chenyu Li ◽

Xiaoming Wang ◽

Zhuosong Cao ◽

Chao Gao ◽

...

Keyword(s):

Antibiotic Resistance ◽

River Water ◽

Resistance Genes ◽

Northeast China ◽

Pathogenic Bacteria ◽

Respiratory Infections ◽

Antibiotic Resistance Genes ◽

Distribution Characteristics ◽

Beta Lactam ◽

Three Rivers

Abstract Background: Antibiotic resistance genes (ARGs) have become an important public health problem. In this study, we used metagenomic sequencing to analyze the composition of ARGs in certain original habitats of northeast China, comprising three different rivers and riverbank soils of the Heilongjiang River, Tumen River, and Yalu River. Results: Twenty types of ARG were detected in every water sample. The major ARGs were multidrug resistance genes, at approximately 0.5 copies/16s rRNA, accounting for 57.5% of the total ARG abundance. The abundance of multidrug, bacitracin, beta-lactam, macrolide‑lincosamide‑streptogramin, sulfonamide, fosmidomycin, and polymyxin resistance genes covered 96.9% of the total ARG abundance. No significant ecological boundary of ARG diversity was observed. The compositions of the resistance genes in the three rivers were very similar to each other, and 92.1% of ARG subtypes were shared by all water samples. Except for vancomycin resistance genes, almost all ARGs in riverbank soils were detected in the river water. About 31.05% ARGs were carried by Pseudomonas. Opportunistic pathogenic bacteria carrying resistance genes were mainly related to diarrhea and respiratory infections. Multidrug and beta-lactam resistance genes correlated positively with mobile genetic elements (MGEs), indicating a potential risk of diffusion.Conclusions: The composition of ARGs in three different rivers was similar, indicating that climate played an important role in ARG occurrence. ARG subtypes in river water were almost completely the same as those in riverbank soil. ARGs had no significant geographical distribution characteristics. Many ARGs were carried by human pathogenic bacteria related to human diarrhea and respiratory infections, such as Pseudomonas aeruginosa and Aeromonas caviae. In general, our results provide a valuable dataset of river water ARG distribution in northeast China. The related ecological geography distribution characteristics should be further explored.

Download Full-text

Effect of frameshift mutagen acriflavine on control of resistance genes in Acinetobacter baumannii

Journal of Medical Microbiology ◽

10.1099/jmm.0.025544-0 ◽

2011 ◽

Vol 60 (2) ◽

pp. 211-215 ◽

Cited By ~ 8

Author(s):

B. S. Lopes ◽

A. Hamouda ◽

J. Findlay ◽

S. G. B. Amyes

Keyword(s):

Gene Expression ◽

Antibiotic Resistance ◽

Acinetobacter Baumannii ◽

Resistance Genes ◽

Outer Membrane Proteins ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

The Body

Acinetobacter baumannii is a Gram-negative pathogenic bacterium that often exhibits a multidrug-resistant phenotype causing infections at various sites of the body and increasingly leading to septicaemic shock. This study evaluated the role of acriflavine, a frameshift mutagen, on the movement of insertion sequence ISAba1 in clinical isolates of A. baumannii, with the focus on changes in expression levels of the bla ADC and bla OXA-51-like genes. Resistance profiles were assessed with consideration of ISAba1 acting as a promoter upstream of the bla ADC or bla OXA-51-like gene. ISAba1 movement was observed in the acriflavine mutants Ab153M and Ab1225M. Ab153M exhibited an increase in the MIC values of carbapenems and ceftazidime, with ISAba1 gained upstream of the bla ADC and bla OXA-51-like genes, correlating with an increase in gene expression. Reduced expression of the 17, 23 and 25 kDa outer-membrane proteins (OMPs) was also observed in Ab153M. There was a significant decrease in MIC values of carbapenems with the loss of ISAba1 upstream of the bla ADC and bla OXA-51-like genes in strain Ab1225M, and a significant decrease in bla OXA-51-like gene expression and, to a lesser extent, in bla ADC expression. Ab1225M and a serially subcultured Ab1225 strain (Ab1225s) exhibited overexpression of the 17, 23, 25 and 27 kDa OMPs. There was a decrease in MIC values of the carbapenems and piperacillin/tazobactam but not of ceftazidime in Ab1225s, which had ISAba1 upstream of the bla ADC and bla OXA-51-like genes. A significant decrease in bla OXA-51-like expression was observed in Ab1225s, whereas the expression of bla ADC was similar to that in the Ab1225 parental strain. The attenuation in this strain may be due to overexpression of OMPs and it is clear that, even if ISAba1 is present upstream of an antibiotic resistance gene, it may not necessarily contribute towards the overexpression of antibiotic resistance genes (bla OXA-51-like in Ab1225s). Movement of the IS element within the A. baumannii chromosome may be an important regulatory mechanism employed by the bacterium under particular stress conditions, and the ability to upregulate the expression of antibiotic resistance genes is likely to be an important factor in the pathogenicity of this bacterium.

Download Full-text

Monitoring and Evaluation of Antibiotic Resistance Genes in Three Rivers in Northeast China

10.21203/rs.3.rs-313046/v1 ◽

2021 ◽

Author(s):

Chen Zhao ◽

Chenyu Li ◽

Xiaoming Wang ◽

Zhuosong Cao ◽

Chao Gao ◽

...

Keyword(s):

Antibiotic Resistance ◽

River Water ◽

Resistance Genes ◽

Northeast China ◽

Pathogenic Bacteria ◽

Respiratory Infections ◽

Antibiotic Resistance Genes ◽

Distribution Characteristics ◽

Beta Lactam ◽

Three Rivers

Download Full-text

Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China

Scientific Reports ◽

10.1038/s41598-020-72620-4 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

YiMing Li ◽

WeiWei Cao ◽

ShuLi Liang ◽

Shinji Yamasaki ◽

Xun Chen ◽

...

Keyword(s):

Antibiotic Resistance ◽

Bacterial Community ◽

Resistance Genes ◽

Southern China ◽

Variation Partitioning ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Food Samples ◽

Rrna Gene

Abstract Ready-to-eat (RTE) foods have been considered to be reservoirs of antibiotic resistance bacteria, which constitute direct threat to human health, but the potential microbiological risks of RTE foods remain largely unexplored. In this study, the metagenomic approach was employed to characterize the comprehensive profiles of bacterial community and antibiotic resistance gene (ARG) in 18 RTE food samples (8 RTE meat, 7 RTE vegetables and 3 RTE fruit) in southern China. In total, the most abundant phyla in RTE foods were Proteobacteria, Firmicutes, Cyanobacteria, Bacteroidetes and Actinobacteria. 204 ARG subtypes belonging to 18 ARG types were detected with an abundance range between 2.81 × 10−5 and 7.7 × 10−1 copy of ARG per copy of 16S rRNA gene. Multidrug-resistant genes were the most predominant ARG type in the RTE foods. Chloramphenicol, macrolide-lincosamide-streptogramin, multidrug resistance, aminoglycoside, bacitracin, tetracycline and β-lactam resistance genes were dominant, which were also associated with antibiotics used extensively in human medicine or veterinary medicine/promoters. Variation partitioning analysis indicated that the join effect of bacterial community and mobile genetic elements (MGEs) played an important role in the resistome alteration. This study further deepens the comprehensive understanding of antibiotic resistome and the correlations among the antibiotic resistome, microbiota, and MGEs in the RTE foods.

Download Full-text

Characterization of Pathogenic Bacteria Isolated from Sudanese Banknotes and Determination of Their Resistance Profile

International Journal of Microbiology ◽

10.1155/2018/4375164 ◽

2018 ◽

Vol 2018 ◽

pp. 1-7 ◽

Cited By ~ 2

Author(s):

Noha Ahmed Abd Alfadil ◽

Malik Suliman Mohamed ◽

Manal M. Ali ◽

El Amin Ibrahim El Nima

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Bacterial Infections ◽

Pathogenic Bacteria ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Diffusion Method ◽

Contamination Level ◽

Rdna Sequencing ◽

Resistant Strains

Background. Banknotes are one of the most exchangeable items in communities and always subject to contamination by pathogenic bacteria and hence could serve as vehicle for transmission of infectious diseases. This study was conducted to assess the prevalence of contamination by pathogenic bacteria in Sudanese banknotes, determine the susceptibility of the isolated organisms towards commonly used antibiotics, and detect some antibiotic resistance genes.Methods. This study was carried out using 135 samples of Sudanese banknotes of five different denominations (2, 5, 10, 20, and 50 Sudanese pounds), which were collected randomly from hospitals, food sellers, and transporters in all three districts of Khartoum, Bahri, and Omdurman. Bacterial prevalence was determined using culture-based techniques, and their sensitivity patterns were determined using the Kirby–Bauer disk diffusion method. Genotypic identification was carried out using PCR and 16S rDNA sequencing. Antibiotic resistance genes of some isolates were detected using PCR technique.Results. All Sudanese banknotes were found to be contaminated with pathogenic bacteria.Klebsiella pneumoniaewas found to be the most frequent isolate (23%), whereasBacillus mycoides(15%) was the most abundant Gram-positive isolate. There was a significant relationship between the number of isolates and the banknote denomination withpvalue <0.05 (the lower denomination showed higher contamination level). Our study has isolated bacteria that are resistant to penicillins and cephalosporins. Multidrug-resistant strains harboring resistant genes (mecA,blaCTX-M, andblaTEM) were also detected.Conclusion. All studied Sudanese banknotes were contaminated with pathogenic bacteria, including multidrug-resistant strains, and may play a significant role in the transmission of bacterial infections.

Download Full-text

Whole Genome Sequencing and Beta-Lactam Resistant Genes in Klebsiella pneumoniae Strains Clinically Isolated from CU Shah Hospital, Gujarat, India

Bioscience Biotechnology Research Communications ◽

10.21786/bbrc/14.4.69 ◽

2021 ◽

Vol 14 (4) ◽

pp. 1847-1854

Author(s):

Vaibhavi Patel

Keyword(s):

Antibiotic Resistance ◽

Klebsiella Pneumoniae ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Virulence Gene ◽

Multidrug Resistant ◽

Whole Genome ◽

Beta Lactam ◽

Resistance Profile ◽

Antibiotic Resistance Profile

A simple explanation for antimicrobial-resistant opportunistic infections in immunocompromised patients is Klebsiella pneumoniae which gradually being associated in insidious infections globally with high mortality rate. Eight hundred fifty-six antibiotic resistant K. pneumoniae isolates were collected over 3 years period (from different wards and different specimens) from the Microbiology department of C.U. Shah hospital, whose AST checked by Kirby Bauer disk diffusion method. To study AMR genes, virulome, interference of virulence gene with resistance gene, phylogenomic; 6 clinical isolates were proceeded for whole genome sequencing and bio informatics analysis. Klebsiella pneumoniae is a multidrug-resistant (MDR) opportunistic and one of delegate of ESKAPE pathogens groups. This pathogen causes nosocomial infections, urinary tract infections, liver abscesses, wound infections, meningitis. These strains obtain a multidrug resistant phenotype by way of horizontal transfer of ARG transported by either transposons or plasmids. This transfer is generally facilitated by Integrons. In this study antibiotic resistance profile and antibiotic resistance genes analysis as well as virulence gene of K. pneumoniae strains were investigated. The study was carried out using 853 clinical isolates collected during 3 years from C.U. Shah hospital of Surendranagar. Antibiotic resistance profile test was carried out by the VITEK 2 against 21 antibiotics. Out of that 6 samples were proceed for DNA extraction, WGS illumina sequencer and analysis of those raw sequences by TORMES pipeline. In this study antibiotic resistance profile included 13 beta lactam antibiotics which classified under 3 class (Penicillin, Cephalosporin, Carbapenem) of beta lactam and in AMR gene study got total 15 different ESBL resistance genes from 6 different klebsiella pneumoniae strain. All these genes detected with more than 90% identity by CARD. (TORMES Pipeline) CTX-M-15, NDM-5, OKP-B-6, PDC-2, OXA-1, OXA-181, OXA-362, OXA-50, OXA-9, SHV-1, SHV-11, SHV-187, TEM-1, TEM-150. In this study, we’ve analyzed the pattern of antibiotic resistance pattern as a phenotypic characteristic and antibiotic resistance genes as genotypic characteristic and co related the results. As multidrug resistance is a worrying matter, constant observation and regular clinical recognition of resistant bacteria are essential to avoid terrible public health incidents. So, our data should be inferred as a warning for need for prevention and control of the MDR K. pneumoniae in hospital settings.

Download Full-text

Antibiotic Resistance and Pathogenomics of Staphylococci Circulating in Novosibirsk, Russia

Microorganisms ◽

10.3390/microorganisms9122487 ◽

2021 ◽

Vol 9 (12) ◽

pp. 2487

Author(s):

Alevtina Bardasheva ◽

Artem Tikunov ◽

Yuliya Kozlova ◽

Elena Zhirakovskaia ◽

Valeriya Fedorets ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Genome Analysis ◽

Complete Genome ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Macrolide Resistance ◽

Beta Lactam ◽

Methicillin Resistant ◽

Complete Genome Analysis

A total of 394 strains of staphylococci found in humans and pets in Novosibirsk, Siberian Russia, were characterized in terms of antibiotic resistance and corresponding genes. Two coagulase-positive and 17 coagulase-negative species were identified. The majority of isolates, with the exception of S. haemolyticus and hospital S. epidermidis isolates, were sensitive to most of the tested antibiotics, and isolates from pets displayed the lowest level of resistance. Nevertheless, methicillin-resistant (MRS) and/or multidrug-resistant (MDR) isolates were found in all prevailed species, including coagulase-negative. A set of genes corresponding to the detected resistance was identified: mecA (beta-lactam resistance), aac(6′)-Ie-aph(2″)-Ia, aph(3′)-IIIa, ant(4′)-Ia (aminoglycoside-modifying enzymes), ermA/ermC, and msrA (macrolide resistance). Complete genome analysis for ten MDR S. epidermidis and five MDR S. haemolyticus isolates revealed additional antibiotic resistance genes mphC, qacA/qacB, norA, dfrC/dfrG, lnuA, BseSR, and fosB. NorA, dfrC, and fosB were present in all S. epidermidis genomes, whereas mphC and msrA were identified in all S. haemolyticus ones. All investigated MDR S. epidermidis and four of five S. haemolyticus strains were moderate or strong biofilm producers, whereas multiple genes responsible for this function and for virulence and pathogenicity were identified mostly in S. epidermidis, but were less frequently represented in S. haemolyticus.

Download Full-text