Characterisation of Bacterial Isolates from Infected Post-Operative Patients in a Malaysian Tertiary Heart Care Centre

Several bacterial species cause post-operative infections, which has been a critical health concern among hospital patients. Our study in this direction is a much-needed exploratory study that was carried out at the National Heart Institute (IJN) of Malaysia to examine the virulence properties of causative bacteria obtained from postoperative patients. The bacterial isolates and data were provided by the IJN. Antibiotic resistance gene patterns, and the ability to form biofilm were investigated for 127 isolates. Klebsiella pneumoniae (36.2%) was the most common isolate collected, which was followed by Pseudomonas aeruginosa (26%), Staphylococcus aureus (23.6%), Streptococcus spp. (8.7%) and Acinetobacter baumannii (5.5%). There were 49 isolates that showed the presence of multidrug resistance genes. The mecA gene was surprisingly found in methicillin-susceptible S. aureus (MSSA), which also carried the ermA gene from those erythromycin-susceptible strains. The phenotypic antibiotic resistance profiles varied greatly between isolates. Findings from the biofilm assay revealed that 44 of the 127 isolates demonstrated the ability to produce biofilms. Our findings provide insights into the possibility of some of these bacteria surviving under antibiotic stress, and some antibiotic resistance genes being silenced.

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Analytical Performance of Multiplexed Screening Test for 10 Antibiotic Resistance Genes from Perianal Swab Samples

Clinical Chemistry ◽

10.1373/clinchem.2015.246371 ◽

2016 ◽

Vol 62 (2) ◽

pp. 353-359 ◽

Cited By ~ 7

Author(s):

G Terrance Walker ◽

Tony J Rockweiler ◽

Rossio K Kersey ◽

Kelly L Frye ◽

Susan R Mitchner ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Test Performance ◽

Health Care Systems ◽

Bacterial Species ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Resistant Bacteria ◽

Gene Test

Abstract BACKGROUND Multiantibiotic-resistant bacteria pose a threat to patients and place an economic burden on health care systems. Carbapenem-resistant bacilli and extended-spectrum β-lactamase (ESBL) producers drive the need to screen infected and colonized patients for patient management and infection control. METHODS We describe a multiplex microfluidic PCR test for perianal swab samples (Acuitas® MDRO Gene Test, OpGen) that detects the vancomycin-resistance gene vanA plus hundreds of gene subtypes from the carbapenemase and ESBL families Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM), Verona integron-mediated metallo-β-lactamase (VIM), imipenemase metallo-β-lactamase (IMP), OXA-23, OXA-48, OXA-51, CTX-M-1, and CTX-M-2, regardless of the bacterial species harboring the antibiotic resistance. RESULTS Analytical test sensitivity per perianal swab is 11–250 CFU of bacteria harboring the antibiotic resistance genes. Test throughput is 182 samples per test run (1820 antibiotic resistance gene family results). We demonstrate reproducible test performance and 100% gene specificity for 265 clinical bacterial organisms harboring a variety of antibiotic resistance genes. CONCLUSIONS The Acuitas MDRO Gene Test is a sensitive, specific, and high-throughput test to screen colonized patients and diagnose infections for several antibiotic resistance genes directly from perianal swab samples, regardless of the bacterial species harboring the resistance genes.

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Metagenomics Analysis Reveals the Microbial Communities, Antimicrobial Resistance Gene Diversity and Potential Pathogen Transmission Risk of Two Different Landfills in China

Diversity ◽

10.3390/d13060230 ◽

2021 ◽

Vol 13 (6) ◽

pp. 230

Author(s):

Shan Wan ◽

Min Xia ◽

Jie Tao ◽

Yanjun Pang ◽

Fugen Yu ◽

...

Keyword(s):

Antibiotic Resistance ◽

Microbial Communities ◽

Resistance Gene ◽

Resistance Genes ◽

Gene Diversity ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Pathogen Transmission ◽

Transmission Risk ◽

Antimicrobial Resistance Gene

In this study, we used a metagenomic approach to analyze microbial communities, antibiotic resistance gene diversity, and human pathogenic bacterium composition in two typical landfills in China. Results showed that the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in the two landfills, and archaea and fungi were also detected. The genera Methanoculleus, Lysobacter, and Pseudomonas were predominantly present in all samples. sul2, sul1, tetX, and adeF were the four most abundant antibiotic resistance genes. Sixty-nine bacterial pathogens were identified from the two landfills, with Klebsiella pneumoniae, Bordetella pertussis, Pseudomonas aeruginosa, and Bacillus cereus as the major pathogenic microorganisms, indicating the existence of potential environmental risk in landfills. In addition, KEGG pathway analysis indicated the presence of antibiotic resistance genes typically associated with human antibiotic resistance bacterial strains. These results provide insights into the risk of pathogens in landfills, which is important for controlling the potential secondary transmission of pathogens and reducing workers’ health risk during landfill excavation.

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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.

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Degradation of antibiotic resistance genes and mobile gene elements in dairy manure anerobic digestion

PLoS ONE ◽

10.1371/journal.pone.0254836 ◽

2021 ◽

Vol 16 (8) ◽

pp. e0254836

Author(s):

Yi Wang ◽

Pramod K. Pandey ◽

Sundaram Kuppu ◽

Richard Pereira ◽

Sharif Aly ◽

...

Keyword(s):

Antibiotic Resistance ◽

Anaerobic Digestion ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Dairy Manure ◽

Health Concern ◽

Animal Origin ◽

Rrna Gene ◽

Transposase Gene ◽

Integrase Gene

Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins–Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.

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Emerging MDR-Pseudomonas aeruginosa in fish commonly harbor oprL and toxA virulence genes and blaTEM, blaCTX-M, and tetA antibiotic-resistance genes

Scientific Reports ◽

10.1038/s41598-020-72264-4 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 4

Author(s):

Abdelazeem M. Algammal ◽

Mahmoud Mabrok ◽

Elayaraja Sivaramasamy ◽

Fatma M. Youssef ◽

Mona H. Atwa ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Virulence Genes ◽

Antibiotic Resistance Genes ◽

Health Concern ◽

Diffusion Method ◽

Multi Drug Resistance ◽

Fish Farms ◽

M Gene ◽

Total Prevalence

Abstract This study aimed to investigate the prevalence, antibiogram of Pseudomonasaeruginosa (P.aeruginosa), and the distribution of virulence genes (oprL,exoS, phzM, and toxA) and the antibiotic-resistance genes (blaTEM, tetA, and blaCTX-M). A total of 285 fish (165 Oreochromisniloticus and 120 Clariasgariepinus) were collected randomly from private fish farms in Ismailia Governorate, Egypt. The collected specimens were examined bacteriologically. P. aeruginosa was isolated from 90 examined fish (31.57%), and the liver was the most prominent infected organ. The antibiogram of the isolated strains was determined using a disc diffusion method, where the tested strains exhibited multi-drug resistance (MDR) to amoxicillin, cefotaxime, tetracycline, and gentamicin. The PCR results revealed that all the examined strains harbored (oprL and toxA) virulence genes, while only 22.2% were positive for the phzM gene. On the contrary, none of the tested strains were positive for the exoS gene. Concerning the distribution of the antibiotic resistance genes, the examined strains harbored blaTEM, blaCTX-M, and tetA genes with a total prevalence of 83.3%, 77.7%, and 75.6%, respectively. Experimentally infected fish with P.aeruginosa displayed high mortalities in direct proportion to the encoded virulence genes and showed similar signs of septicemia found in the naturally infected one. In conclusion, P.aeruginosa is a major pathogen of O.niloticus and C.gariepinus.oprL and toxA genes are the most predominant virulence genes associated with P.aeruginosa infection. The blaCTX-M,blaTEM, and tetA genes are the main antibiotic-resistance genes that induce resistance patterns to cefotaxime, amoxicillin, and tetracycline, highlighting MDR P.aeruginosa strains of potential public health concern.

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Predicting Antibiotic Resistance in Gram-Negative Bacilli from Resistance Genes

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02462-18 ◽

2019 ◽

Vol 63 (4) ◽

Cited By ~ 3

Author(s):

G. Terrance Walker ◽

Julia Quan ◽

Stephen G. Higgins ◽

Nikhil Toraskar ◽

Weizhong Chang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Unknown Origin ◽

Bacterial Isolates ◽

Antibiotic Resistant ◽

Predictive Values ◽

Content Type ◽

Phenotypic Resistance ◽

E Coli

ABSTRACT We developed a rapid high-throughput PCR test and evaluated highly antibiotic-resistant clinical isolates of Escherichia coli (n = 2,919), Klebsiella pneumoniae (n = 1,974), Proteus mirabilis (n = 1,150), and Pseudomonas aeruginosa (n = 1,484) for several antibiotic resistance genes for comparison with phenotypic resistance across penicillins, cephalosporins, carbapenems, aminoglycosides, trimethoprim-sulfamethoxazole, fluoroquinolones, and macrolides. The isolates originated from hospitals in North America (34%), Europe (23%), Asia (13%), South America (12%), Africa (7%), or Oceania (1%) or were of unknown origin (9%). We developed statistical methods to predict phenotypic resistance from resistance genes for 49 antibiotic-organism combinations, including gentamicin, tobramycin, ciprofloxacin, levofloxacin, trimethoprim-sulfamethoxazole, ertapenem, imipenem, cefazolin, cefepime, cefotaxime, ceftazidime, ceftriaxone, ampicillin, and aztreonam. Average positive predictive values for genotypic prediction of phenotypic resistance were 91% for E. coli, 93% for K. pneumoniae, 87% for P. mirabilis, and 92% for P. aeruginosa across the various antibiotics for this highly resistant cohort of bacterial isolates.

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Removal of Antibiotic Resistance Gene-Carrying Plasmids from Lactobacillus reuteri ATCC 55730 and Characterization of the Resulting Daughter Strain, L. reuteri DSM 17938

Applied and Environmental Microbiology ◽

10.1128/aem.00991-08 ◽

2008 ◽

Vol 74 (19) ◽

pp. 6032-6040 ◽

Cited By ~ 146

Author(s):

Anna Rosander ◽

Eamonn Connolly ◽

Stefan Roos

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Lactobacillus Reuteri ◽

Antibiotic Resistance Gene ◽

Genetically Modify ◽

Antibiotic Resistance Genes ◽

Probiotic Strain ◽

Probiotic Properties ◽

Food Borne

ABSTRACT The spread of antibiotic resistance in pathogens is primarily a consequence of the indiscriminate use of antibiotics, but there is concern that food-borne lactic acid bacteria may act as reservoirs of antibiotic resistance genes when distributed in large doses to the gastrointestinal tract. Lactobacillus reuteri ATCC 55730 is a commercially available probiotic strain which has been found to harbor potentially transferable resistance genes. The aims of this study were to define the location and nature of β-lactam, tetracycline, and lincosamide resistance determinants and, if they were found to be acquired, attempt to remove them from the strain by methods that do not genetically modify the organism before subsequently testing whether the probiotic characteristics were retained. No known β-lactam resistance genes was found, but penicillin-binding proteins from ATCC 55730, two additional resistant strains, and three sensitive strains of L. reuteri were sequenced and comparatively analyzed. The β-lactam resistance in ATCC 55730 is probably caused by a number of alterations in the corresponding genes and can be regarded as not transferable. The strain was found to harbor two plasmids carrying tet(W) tetracycline and lnu(A) lincosamide resistance genes, respectively. A new daughter strain, L. reuteri DSM 17938, was derived from ATCC 55730 by removal of the two plasmids, and it was shown to have lost the resistances associated with them. Direct comparison of the parent and daughter strains for a series of in vitro properties and in a human clinical trial confirmed the retained probiotic properties of the daughter strain.

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Antibiotic resistance genes in phage particles isolated from human faeces and induced from clinical bacterial isolates

International Journal of Antimicrobial Agents ◽

10.1016/j.ijantimicag.2017.11.014 ◽

2018 ◽

Vol 51 (3) ◽

pp. 434-442 ◽

Cited By ~ 21

Author(s):

Maryury Brown-Jaque ◽

William Calero-Cáceres ◽

Paula Espinal ◽

Judith Rodríguez-Navarro ◽

Elisenda Miró ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Bacterial Isolates ◽

Human Faeces

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RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids

mSystems ◽

10.1128/msystems.00349-18 ◽

2019 ◽

Vol 4 (1) ◽

Cited By ~ 6

Author(s):

Taylor K. Dunivin ◽

Jinlyung Choi ◽

Adina Howe ◽

Ashley Shade

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Soil Microorganisms ◽

Antibiotic Resistance Genes ◽

Health Concern ◽

Reference Database ◽

Chromosome Size ◽

Microbial Strains ◽

Plasmid Size ◽

Host Associations

ABSTRACT Plasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve the understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were larger than other described plasmids, which is a trait associated with plasmid mobility. There was a weak relationship between chromosome size and plasmid size and no relationship between chromosome size and plasmid number, suggesting that these genomic traits are independent in soil. We used RefSoil+ to inform the distributions of antibiotic resistance genes among soil microorganisms compared to those among nonsoil microorganisms. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a reference for the diversity, composition, and host associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves the understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances. IMPORTANCE Soil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource of important plasmid-associated genes, including antibiotic resistance genes.

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Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis

mSystems ◽

10.1128/msystems.00821-19 ◽

2020 ◽

Vol 5 (3) ◽

Cited By ~ 3

Author(s):

Yu Pan ◽

Jiaxiong Zeng ◽

Liguan Li ◽

Jintao Yang ◽

Ziyun Tang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Virulence Factors ◽

Resistance Genes ◽

Large Scale ◽

Antibiotic Resistance Genes ◽

Comprehensive Analysis ◽

Health Concern ◽

Human Pathogens ◽

Bacterial Genomes ◽

Gene Acquisition

ABSTRACT Widespread use of antibiotics has enhanced the evolution of highly resilient pathogens and poses a severe risk to human health via coselection of antibiotic resistance genes (ARGs) and virulence factors (VFs). In this study, we rigorously evaluate the abundance relationship and physical linkage between ARGs and VFs by performing a comprehensive analysis of 9,070 bacterial genomes isolated from multiple species and hosts. The coexistence of ARGs and VFs was observed in bacteria across distinct phyla, pathogenicities, and habitats, especially among human-associated pathogens. The coexistence patterns of gene elements in different habitats and pathogenicity groups were similar, presumably due to frequent gene transfer. A shorter intergenic distance between mobile genetic elements and ARGs/VFs was detected in human/animal-associated bacteria, indicating a higher transfer potential. Increased accumulation of exogenous ARGs/VFs in human pathogens highlights the importance of gene acquisition in the evolution of human commensal bacteria. Overall, the findings provide insights into the genic features of combinations of ARG-VF and expand our understanding of ARG-VF coexistence in bacteria. IMPORTANCE Antibiotic resistance has become a serious global health concern. Despite numerous case studies, a comprehensive analysis of ARG and VF coexistence in bacteria is lacking. In this study, we explore the coexistence profiles of ARGs and VFs in diverse categories of bacteria by using a high-resolution bioinformatics approach. We also provide compelling evidence of unique ARG-VF gene pairs coexisting in specific bacterial genomes and reveal the potential risk associated with the coexistence of ARGs and VFs in organisms in both clinical settings and environments.

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