scholarly journals High Diversity of Extended-Spectrum Beta-Lactamase-Producing Bacteria in an Urban River Sediment Habitat

2010 ◽  
Vol 76 (17) ◽  
pp. 5972-5976 ◽  
Author(s):  
Su-Ying Lu ◽  
Ya-Li Zhang ◽  
Sui-Na Geng ◽  
Tian-Yu Li ◽  
Zhuo-Ming Ye ◽  
...  
Keyword(s):  
River Sediment ◽  
16S Rrna Gene Sequencing ◽  
Urban River ◽  
Resistant Bacteria ◽  
Rrna Gene ◽  
Antibiotic Resistant ◽  
Extended Spectrum Beta Lactamase ◽  
Extended Spectrum ◽  
Rrna Gene Sequencing ◽  
First Time

ABSTRACT Antibiotic-resistant bacteria (ARB) have been surveyed widely in water bodies, but few studies have determined the diversity of ARB in sediment, which is the most taxon-abundant habitat in aquatic environments. We isolated 56 extended-spectrum β-lactamase (ESBL)-producing bacteria from a single sediment sample taken from an urban river in China. All strains were confirmed for ESBL-producing capability by both the clavulanic acid combination disc method and MIC determination. Of the isolated strains, 39 were classified as Enterobacteriaceae (consisting of the genera Escherichia, Klebsiella, Serratia, and Aeromonas) by 16S rRNA gene sequencing and biochemical analysis. The present study identifies, for the first time, ESBL-producing strains from the families Brucellaceae and Moraxellaceae. The bla CTX-M gene was the most dominant of the ESBL genes (45 strains), while the bla TEM gene was the second-most dominant (22 strains). A total of five types of bla CTX-M fragments were identified, with both known and novel sequences. A library of bla CTX-M cloned from the sediment DNA showed an even higher diversity of bla CTX-M sequences. The discovery of highly diverse ESBL-producing bacteria and ESBL genes, particularly bla CTX, in urban river sediment raises alarms for potential dissemination of ARB in communities through river environments.

scholarly journals Multi-Drug Resistance Bacteria: A Case Study in Western Peninsular Malaysia Freshwaters

2021 ◽  
Vol 11 (3) ◽  
pp. 285-297
Author(s):  
Mohd Suhaimi ◽  
◽  
Kam Yern ◽  
Mohd Kamaroddin ◽  
Syahidatul Rizal ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Peninsular Malaysia ◽  
Resistant Bacteria ◽  
Rrna Gene ◽  
Antibiotic Resistant ◽  
Mar Index ◽  
Rrna Gene Sequencing ◽  
Index Value

The emergence of antibiotic resistant bacteria in aquatic environment has led to an increase in waterborne health risks to an alarming extent. This study attempts to investigate the population of certain antibiotic resistant strains in Peninsular Malaysia. From the samples of 14 rivers from 7 different states in Peninsular Malaysia, a total of 203 isolates were successfully isolated. These are from rivers in Negeri Sembilan, Melaka, Selangor, Kuala Lumpur, Kedah, Kelantan and Terengganu with 35, 15, 37, 39, 24, 26 and 27 isolates, respectively. The isolates were tested for their susceptibility towards 6 broad spectrum of antibiotics which are gentamicin, ampicillin, rifampicin, chloramphenicol, tetracycline, and ciprofloxacin. A total of 117 isolates were identified to have more than 20% MAR index value with 47 of the isolates possess minimum MAR index value of 50%. Based on MAR index value, 59% of isolates are high risk threats indicating a serious emergence of antibiotic resistant bacteria in the rivers in Peninsular Malaysia. Isolates with MAR index value of more than 50% were selected for 16S rRNA gene sequencing for further identification.Based on 16s rRNA gene sequencing, the isolates are a mixture of pathogenic and commensals bacteria. This also implies that the environment especially rivers can be a reservoir for genetic jugglery

Characterization of bacteria and antibiotic resistance in commercially-produced cheeses sold in China

2021 ◽  
Author(s):  
Jinghui Yao ◽  
Jing Gao ◽  
Jianming Guo ◽  
Hengan Wang ◽  
En Zhang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Acquired Resistance ◽  
Antibiotic Resistance Genes ◽  
16S Rrna Gene Sequencing ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

The consumption of cheese in China is increasing rapidly. Little is known about the microbiota, the presence of antibiotic-resistant bacteria, or the distribution of antibiotic resistance genes (ARGs) in commercially-produced cheeses sold in China. These are important criteria for evaluating quality and safety. Thus, this study assessed the metagenomics of fifteen types of cheese using 16S rRNA gene sequencing. Fourteen bacterial genera were detected. Lactococcus , Lactobacillus , and Streptococcus were dominant based on numbers of sequence reads. Multidrug-resistant lactic acid bacteria were isolated from most of the types of cheese. The isolates showed 100% and 91.7% resistance to streptomycin and sulfamethoxazole, respectively, and genes involved in acquired resistance to streptomycin ( strB) and sulfonamides ( sul2) were detected with high frequency. To analyze the distribution of ARGs in the cheeses in overall, 309 ARGs from eight categories of ARG and nine transposase genes were profiled. A total of 169 ARGs were detected in the 15 cheeses; their occurrence and abundance varied significantly between cheeses. Our study demonstrates that there is various diversity of the bacteria and ARGs in cheeses sold in China. The risks associated with multidrug resistance of dominant lactic acid bacteria are of great concern.

scholarly journals Extended-Spectrum Beta-Lactamase Gene Sequences in Gram-Negative Saprophytes on Retail Organic and Nonorganic Spinach

2011 ◽  
Vol 77 (5) ◽  
pp. 1601-1607 ◽  
Author(s):  
Eva Raphael ◽  
Lisa K. Wong ◽  
Lee W. Riley
Keyword(s):  
Drug Resistance ◽  
Resistance Genes ◽  
16S Rrna Gene Sequencing ◽  
Drug Susceptibility Testing ◽  
Rrna Gene ◽  
Beta Lactamase ◽  
Human Pathogens ◽  
Gram Negative ◽  
Extended Spectrum Beta Lactamase ◽  
Extended Spectrum

ABSTRACTA substantial proportion of infections caused by drug-resistant Gram-negative bacteria (GNB) in community and health care settings are recognized to be caused by evolutionarily related GNB strains. Their global spread has been suggested to occur due to human activities, such as food trade and travel. These multidrug-resistant GNB pathogens often harbor mobile drug resistance genes that are highly conserved in their sequences. Because they appear across different GNB species, these genes may have origins other than human pathogens. We hypothesized that saprophytes in common human food products may serve as a reservoir for such genes. Between July 2007 and April 2008, we examined 25 batches of prepackaged retail spinach for cultivatable GNB population structure by 16S rRNA gene sequencing and for antimicrobial drug susceptibility testing and the presence of extended-spectrum beta-lactamase (ESBL) genes. We found 20 recognized GNB species among 165 (71%) of 231 randomly selected colonies cultured from spinach. Twelve strains suspected to express ESBLs based on resistance to cefotaxime and ceftazidime were further examined forblaCTX-MandblaTEMgenes. We found a 712-bp sequence inPseudomonas teessideathat was 100% identical to positions 10 to 722 of an 876-bpblaCTX-M-15gene of anE. colistrain. Additionally, we identified newly recognized ESBLblaRAHN-2sequences fromRahnella aquatilis. These observations demonstrate that saprophytes in common fresh produce can harbor drug resistance genes that are also found in internationally circulating strains of GNB pathogens; such a source may thus serve as a reservoir for drug resistance genes that ultimately enter pathogens to affect human health.

scholarly journals Phenotypic and molecular characterization of multidrug-resistant extended-spectrum beta-lactamase-producing Salmonella prevalent in raw chicken meat vended in Nigerian markets

2021 ◽  
Vol 32 (1) ◽  
pp. 76-84
Author(s):  
Gideon Ikechechukwu Ogu ◽  
Faith Iguodala Akinnibosun ◽  
Odaro Stanley Imade
Keyword(s):  
Salmonella Enterica ◽  
16S Rrna Gene Sequencing ◽  
Multidrug Resistant ◽  
Chicken Meat ◽  
Rrna Gene ◽  
Meat Industry ◽  
Beta Lactamase ◽  
Modeling Tool ◽  
Extended Spectrum Beta Lactamase ◽  
Extended Spectrum

Abstract In Nigeria, there is still a scarcity of data on the recovery of multidrug-resistant ESBL-producing Salmonella in chicken meat. Hence this study characterized the probable multidrug-resistant extended-spectrum beta-lactamase-producing Salmonella prevalent in chilled raw chicken meat vended in Nigerian markets. Detection of Salmonella was performed by meat rinse centrifugation-plating technique. Presumptive Salmonella colonies were identified by phenotypic and 16S rRNA gene sequencing. The confirmed Salmonella isolates were tested for multidrug resistance by the Kirby Bauer disc diffusion test. Detection and confirmation of extended-spectrum beta-lactamase (ESBL) phenotypes were performed by double disc synergy and combination disc tests. PCR and DNA sequencing of the ESBL-encoding genes (bla SHV, bla TEM, and bla CTX-M) were also performed. The conserved and three-dimensional (3D) domains in ESBLs were respectively characterized by the reverse position-specific BLAST (RPS-BLAST) and Cn3D modeling tool. Of the 229 presumptive Salmonella isolates examined, 52 isolates were confirmed as Salmonella species, 46 isolates were multidrug-resistant and 41 isolates confirmed as multidrug-resistant ESBL-producing Salmonella species. The main serotypes were Salmonella enterica subsp. enterica serovar Typhimurium (35/52; 67.31%) and Salmonella enterica subsp. enterica serovar Enteritidis (17/52; 32.69%). Overall, the prevalence of chilled raw chicken meat contaminated with Salmonella was estimated at 0.17 (40/240). This value of prevalence exceeded the limits (≤ 0.1) set by the Meat Industry Guide, United Kingdom. All CTX-M, TEM, and SHV beta-lactamases produced by the Salmonella isolates were confirmed by RPS-BLAST and Cn3D modeling tool as serine-based hydrolases that consisted of two 3D domains with unique ligands such as sodium ion, formic acid, and glycerol. This study showed that multidrug-resistant ESBL-producing Salmonella was widespread in raw chicken meat vended in Nigerian markets. Thus, there is a need for relevant regulatory agencies to enforce safety.

Fate of two strains of extended-spectrum beta-lactamase producing Escherichia coli in constructed wetland microcosm sediments: survival and change in antibiotic resistance profiles

2019 ◽  
Vol 79 (8) ◽  
pp. 1550-1560 ◽  
Author(s):  
Anne-Laure Vivant ◽  
Catherine Boutin ◽  
Stéphanie Prost-Boucle ◽  
Sandrine Papias ◽  
Christine Ziebal ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Antibiotic Resistance Genes ◽  
Free Water ◽  
Resistant Bacteria ◽  
Rapid Decline ◽  
Beta Lactamase ◽  
Antibiotic Resistant ◽  
Extended Spectrum Beta Lactamase ◽  
Extended Spectrum

Abstract Free water surface constructed wetlands (FWS CW) are efficient technologies to limit the transfer of antibiotic resistant bacteria (ARB) originating from urban effluents into the aquatic environment. However, the decrease in ARB from inflow to outflow through the FWS CW may be explained by their transfer from the water body to the sediment. To investigate the behavior of ARB in the sediment of a FWS CW, we inoculated three microcosms with two strains of extended-spectrum beta-lactamase producing Escherichia coli (ESBL E. coli) belonging to two genotypes. Microcosms were composed of two sediments collected at two locations of an FWS CW from which the strains were isolated. Phragmites were planted in one of the microcosms. The survival curves of the two strains were close regardless of the genotype and the type of sediment. After a rapid decline, both strains were able to survive at low level in the sediments for 50 days. Their fate was not affected by the presence of phragmites. Changes in the bla content and antibiotic resistance of the inoculated strains were observed after three weeks of incubation, indicating that FWS CW sediments are favorable environments for spread of antibiotic resistance genes and for the acquisition of new antibiotic resistance.

scholarly journals Glacier clear ice bands indicate englacial channel microbial distribution

2021 ◽  
pp. 1-13
Author(s):  
Gilda Varliero ◽  
Alexandra Holland ◽  
Gary L. A. Barker ◽  
Marian L. Yallop ◽  
Andrew G. Fountain ◽  
...  
Keyword(s):  
Microbial Communities ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbial Distribution ◽  
Secondary Factor ◽  
Glacier Ice ◽  
Rrna Gene Sequencing ◽  
Surface Ice ◽  
First Time

Abstract Distant glacial areas are interconnected by a complex system of fractures and water channels which run in the glacier interior and characterize the englacial realm. Water can slowly freeze in these channels where the slow freezing excludes air bubbles giving the ice a clear aspect. This ice is uplifted to the surface ablation zone by glacial movements and can therefore be observed in the form of clear surface ice bands. We employed an indirect method to sample englacial water by coring these ice bands. We were able, for the first time, to compare microbial communities sampled from clear (i.e. frozen englacial water bands) and cloudy ice (i.e. meteoric ice) through 16S rRNA gene sequencing. Although microbial communities were primarily shaped and structured by their spatial distribution on the glacier, ice type was a clear secondary factor. One area of the glacier, in particular, presented significant microbial community clear/cloudy ice differences. Although the clear ice and supraglacial communities showed typical cold-adapted glacial communities, the cloudy ice had a less defined glacial community and ubiquitous environmental organisms. These results highlight the role of englacial channels in the microbial dispersion within the glacier and, possibly, in the shaping of glacial microbial communities.

scholarly journals The Carrier Rate of Extended Spectrum Beta Lactamase (ESBL) Producing Bacteria in Cockroaches (Periplaneta americana) in Hospital and Community

2021 ◽  
Vol 57 (4) ◽  
pp. 283
Author(s):  
Ardhiya Puspita ◽  
Radita Yuniar Arizandy ◽  
Eddy Bagus Wasito ◽  
Kuntaman Kuntaman
Keyword(s):  
Periplaneta Americana ◽  
Hospital Environment ◽  
Resistant Bacteria ◽  
Natural Habitats ◽  
Antibiotic Resistant ◽  
Extended Spectrum Beta Lactamase ◽  
Esbl Gene ◽  
Extended Spectrum ◽  
Synergy Test ◽  
Esbl Producers

Highlight :Bacteriologically for colonization of  ESBL producing Enterobacteriaceae in cockroaches (Periplaneta americana) were analyzed.The prevalence of ESBL producing bacteria among cockroaches in hospitals is bigger than in households.Abstract: Cockroach (Periplaneta americana) is one of the vectors in the environment that can transmit disease. Cockroaches can act as potential mechanical vectors of antibiotic resistant bacteria. Enterobacteriaceae is a gram-negative bacteria that has natural habitats in the digestive tract of humans and animals. Enterobacteriaceae that produce Extended Spectrum β-lactamases (ESBLs) have emerged as major pathogens in hospitals. The study analyzed the prevalence of ESBL producing bacteria in cockroaches that lived in hospitals and residential homes. In this study, a total of 200 cockroaches consisting of 100 cockroaches from the hospital environment and 100 cockroaches from the residential environment were analyzed bacteriologically for colonization of  ESBL producing Enterobacteriaceae. The specimen of the alimentary tract was taken and sub-cultured in MacConkey agar supplemented with cefotaxime 2 ug/ml. Growth colonies were suggested as an ESBL-producing bacteria, then were confirmed as ESBL producers by the Double Disk Synergy Test (DDST). The ESBL gene was detected by Polymerase Chain Reaction (PCR). Among 100 household cockroach samples, 14 (14%) were identified as ESBL producers, while 100 hospital cockroaches were 26 (26%) positive ESBL. The ESBL gene, in hospital cockroach were identified of CTXM 19 (19%), SHV 7 (7%), and not any TEM gene, while among household cockroaches were identified CTXM 2 (2%), SHV 11 (11%), and also not detected TEM ESBL gene. Among ESBL genes, only the CTXM gene was significantly different between household and hospital cockroaches.

scholarly journals Antibiotic resistant bacteria and commensal fungi are common and conserved in the mosquito microbiome

2019 ◽  
Author(s):  
Josephine Hyde ◽  
Courtney Gorham ◽  
Doug E. Brackney ◽  
Blaire Steven
Keyword(s):  
Antibiotic Resistance ◽  
Gene Sequencing ◽  
Resistant Bacteria ◽  
Rrna Gene ◽  
28S Rrna ◽  
Antibiotic Resistant Bacteria ◽  
Bacterial Populations ◽  
Antibiotic Resistant ◽  
Cell Counts ◽  
Rrna Gene Sequencing

AbstractThe emerging and increasing prevalence of bacterial antibiotic resistance is a significant public health challenge. To begin to tackle this problem, it will be critical to not only understand the origins of this resistance but also document environmental reservoirs of antibiotic resistance. In this study we investigated the possibility that both colony and field caught mosquitoes could harbor antibiotic resistant bacteria. Specifically, we characterized the antibiotic resistant bacterial populations from colony-reared Aedes aegypti larvae and adults and two field caught mosquito species Coquillettidia perturbans and Ochlerotatus canadensis. The cultured bacterial populations were dominated by isolates belonging to the class Gammaproteobacteria. Among the antibiotic resistant populations, we found bacteria resistant to carbenicillin, kanamycin, and tetracycline, including bacteria resistant to a cocktail of all three antibiotics in combination. The antibiotic resistant bacteria were numerically rare, at most 5% of total cell counts. Isolates were characterized by 16S rRNA gene sequencing, and clustering into Operational Taxonomic Units (OTUs; 99% sequence identity). 27 antibiotic resistant OTUs were identified, although members of an OTU did not always share the same resistance profile. This suggests the clustering was either not sensitive enough to distinguish different bacteria taxa or different antibiotic resistant sub-populations exist within an OTU. Finally, the antibiotic selection opened up a niche to culture mosquito-associated fungi, and 10 fungal OTUs (28S rRNA gene sequencing) were identified. Two fungal OTUs both classified to the class Microbotryomycetes were commonly identified in the field-caught mosquitoes. Thus, in this study we demonstrate that antibiotic resistant bacteria and certain fungi are common and conserved mosquito microbiome members. These observations highlight the potential of invertebrates to serve as vehicles for the spread of antibiotic resistance throughout the environment.

scholarly journals Gut microbiota and fecal metabolites in captive and wild North China leopard (Panthera pardus japonensis) by comparsion using 16s rRNA gene sequencing and LC/MS-based metabolomics

2020 ◽  
Author(s):  
Yan Hua ◽  
Heqin cao ◽  
Jiao Wang ◽  
Fengping He ◽  
Guangshun Jiang
Keyword(s):  
Gut Microbiota ◽  
North China ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Panthera Pardus ◽  
Bacterial Phyla ◽  
Metabolic Phenotypes ◽  
Rrna Gene Sequencing ◽  
First Time

Abstract Background: Gut microbes significantly contribute to nutrient digestion and absorption, intestinal health and immunity, and are essential for the survival and environmental adaptation of wild animals. However, there are few studies on the gut microbiota of captive and wild North China leopard (Panthera pardus japonensis). Results: A total of 10 mainly bacterial phyla were identified in the fecal microbiota of North China leopard, Lachnoclostridium (p = 0.003), Peptoclostridium (p = 0.005), Bacteroides (p =0.008), Fusobacterium (p = 0.017) and Collinsella (p = 0.019) were significantly higher than those of wild North China leopard. Distinct differences in the fecal metabolic phenotypes of captive and wild North China leopard were found, such as content of l-methionine, n-acetyl-l-tyrosine, pentadecanoic acid and oleic acid. Differentially abundant gut microbes were associated with fecal metabolites, especially the bacteria in Firmicutes and Bacteroidetes, involved in the metabolism of N-acetyl-L-alanine and D-quinovose.Conclusion: This study reports for the first time the differences in gut microbiota abundance between captive and wild North China leopard, as well as significant differences in fecal metabolic phenotypes between two groups.

scholarly journals 16S rRNA gene-based metagenomic analysis identifies a novel bacterial co-prevalence pattern in dental caries

2015 ◽  
Vol 09 (01) ◽  
pp. 127-132 ◽  
Author(s):  
Sri Nisha Jagathrakshakan ◽  
Raghavendra Jayesh Sethumadhava ◽  
Dhaval Tushar Mehta ◽  
Arvind Ramanathan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Age Groups ◽  
16S Rrna Gene Sequencing ◽  
Mixed Dentition ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
The Subject ◽  
Rrna Gene Sequencing ◽  
First Time

ABSTRACT Objective: To identify the prevalence of acidogenic and nonacidogenic bacteria in patients with polycaries lesions, and to ascertain caries specific bacterial prevalence in relation to noncaries controls. Materials and Methods: Total genomic DNA extracted from saliva of three adults and four children from the same family were subjected to 16S rRNA gene sequencing analysis on a next generation sequencer, the PGS-Ion Torrent. Those bacterial genera with read counts > 1000 were considered as significant in each of the subject and used to associate the occurrence with caries. Results and Conclusion: Sequencing analysis indicated a higher prevalence of Streptococcus, Rothia, Granulicatella, Gemella, Actinomyces, Selenomonas, Haemophilus and Veillonella in the caries group relative to controls. While higher prevalence of Streptococcus, Rothia and Granulicatella were observed in all caries samples, the prevalence of others was observable in 29–57% of samples. Interestingly, Rothia and Selenomonas, which are known to occur within anaerobic environments of dentinal caries and subgingival plaque biofilms, were seen in the saliva of these caries patients. Taken together, the study has identified for the first time a unique co-prevalence pattern of bacteria in caries patients that may be explored as distinct caries specific bacterial signature to predict cariogenesis in high-risk primary and mixed dentition age groups.

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