Metagenomics-Guided Assessment of Water Quality and Predicting Pathogenic Load

2022 ◽  
pp. 71-91
Author(s):  
Sayak Ganguli ◽  
Rupsha Karmakar ◽  
Meesha Singh ◽  
Mahashweta Mitra Ghosh
Keyword(s):  
Molecular Techniques ◽  
Resistant Bacteria ◽  
Load Prediction ◽  
Antibiotic Resistant ◽  
Comparative Metagenomics ◽  
Tropical Environments ◽  
Culture Independent ◽  
Urban Sample ◽  
Rural Sample ◽  
Irritable Bowel

Antibiotic-resistant bacteria (ARB) are becoming more prevalent in the environment and are efficiently disseminating through contaminated wastewater resulting in resistome cycling. This chapter compares the bacterial profile of hospital effluents collected from rural, urban, and delta regions of West Bengal, India. Comparative metagenomics analysis identified pathogenic bacterial genera like pseudomonas, escherichia, staphylococcus, lactobacillus, prevotella, acinetobacter across the samples. Delta sample showed highest abundance of pseudomonas whereas rural sample had lower titre of all the common bacterial genera. Urban sample reflected more diversity of different genera in terms of abundance. Pathogenic load prediction revealed significant occurrence of diarrhea, irritable bowel syndrome, liver cirrhosis, ulcerative colitis in the disease network. This chapter proposes a monitoring programme for assessing wastewater health using a combination of culture independent and culture-dependent molecular techniques in order to prevent the spread of pollutants in tropical environments.

Microfluidics: innovative approaches for rapid diagnosis of antibiotic-resistant bacteria

2017 ◽  
Vol 61 (1) ◽  
pp. 91-101 ◽  
Author(s):  
Amornrat Aroonnual ◽  
Tavan Janvilisri ◽  
Puey Ounjai ◽  
Surang Chankhamhaengdecha
Keyword(s):  
Point Of Care ◽  
Diagnostic Procedures ◽  
Microfluidic System ◽  
Molecular Techniques ◽  
Health Concern ◽  
Phenotypic Characterization ◽  
Resistant Bacteria ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant ◽  
Diagnostic Strategies

The emergence of antibiotic-resistant bacteria has become a major global health concern. Rapid and accurate diagnostic strategies to determine the antibiotic susceptibility profile prior to antibiotic prescription and treatment are critical to control drug resistance. The standard diagnostic procedures for the detection of antibiotic-resistant bacteria, which rely mostly on phenotypic characterization, are time consuming, insensitive and often require skilled personnel, making them unsuitable for point-of-care (POC) diagnosis. Various molecular techniques have therefore been implemented to help speed up the process and increase sensitivity. Over the past decade, microfluidic technology has gained great momentum in medical diagnosis as a series of fluid handling steps in a laboratory can be simplified and miniaturized on to a small platform, allowing marked reduction of sample amount, high portability and tremendous possibility for integration with other detection technologies. These advantages render the microfluidic system a great candidate to be developed into an easy-to-use sample-to-answer POC diagnosis suitable for application in remote clinical settings. This review provides an overview of the current development of microfluidic technologies for the nucleic acid based and phenotypic-based detections of antibiotic resistance.

scholarly journals 654. Performance of the T2Resistance Panel in Detecting Antibiotic Resistant Bacteria Directly in Whole Blood, and Implications for Improving Appropriate Therapy of Bloodstream Infections

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S429-S429
Author(s):  
Abigail Skeel ◽  
Cornelius J Clancy ◽  
Aaron Lucas ◽  
Kailey L Hughes ◽  
Ryan K Shields ◽  
...  
Keyword(s):  
Blood Culture ◽  
Whole Blood ◽  
Bloodstream Infections ◽  
Resistant Bacteria ◽  
Gram Stain ◽  
Research Support ◽  
Antibiotic Resistant ◽  
Culture Independent ◽  
Appropriate Therapy ◽  
Resistance Markers

Abstract Background Appropriate antibiotic (Ab) therapy of bloodstream infections (BSI) is often delayed by time to blood culture (BC) positivity, species (sp) identification and Ab sensitivity (sensi). The T2Resistance (T2R) Panel is a direct-from-blood (culture-independent) diagnostic that detects 13 genetic markers associated with methicillin-resistant S. aureus (MRSA), vancomycin-resistant Enterococcus (VRE), ESBL- and carbapenemase-producing Enterobacteriaceae (E). We assessed T2R performance in detecting these resistant bacteria in whole blood (WB) and analyzed possible impact on time to appropriate Ab. Methods We performed T2R using WB samples obtained from patients (pts) on the same day as BCs from July 2019-2020. Receipt of appropriate Ab was assessed at time of empiric, Gram stain-directed, MALDI-directed (sp identification) and sensi-directed therapy. T2R results were not available to care teams. Teams were notified of positive BCs. Stewardship optimized Abs based on sensi. Results BC from 103 pts grew 114 bacterial sp: E (n=54; 16 ESBL-, 1 KPC-producer), S. aureus (n=29, 22 MRSA), Enterococcus (n=21, 16 VRE), P. aeruginosa and others (n=10). 12 ESBL-E produced CTX-M 14/15. T2R sensitivity and specificity was 78% and 99%, respectively, compared to sequencing of resistance markers. Sensitivity was excellent for vanA/B, KPC (100% each), and CTX-M14/15 (92%); sensitivity was 58% for mecA/C. T2R detected resistance determinants in 3-7h. Median time to appropriate Ab was 16.3h, which was significantly longer for VRE (25.6h) and ESBL- or KPC-E (50.9h) BSIs than for T2R marker-negative bacteria (6.7h; p=0.04). Pts with VRE or ESBL-/KPC-E BSI were less likely to received appropriate empiric Ab (18% and 30%, respectively) than pts with T2R marker-negative BSI (63%; p=0.02; Fig.1). Median times to achieve ≥80% appropriate Ab therapy of marker-negative, VRE and CTX-M/KPC-E BSIs were 15.5h (after Gram stain), 43.9h (after MALDI) and 63.5h (after sensi), respectively. Antibiotic Therapy Conclusion There was a significant delay in appropriate Ab therapy of BSIs, especially in pts infected with VRE and ESBL/KPC-E. T2R rapidly and accurately detected BSI caused by VRE and ESBL/KPC-E, and has the potential to significantly shorten time to appropriate Ab. Disclosures Cornelius J. Clancy, MD, Merck (Grant/Research Support) Ryan K. Shields, PharmD, MS, Shionogi (Consultant, Research Grant or Support) Minh-Hong Nguyen, MD, Merck (Grant/Research Support)

Relationship of antibiotic resistance to results of treatment in sepsis patients in Hue Central Hospital 2017 – 2018

2019 ◽  
pp. 48-54
Author(s):  
Duy Binh Nguyen ◽  
Trung Tien Phan ◽  
Trong Hanh Hoang ◽  
Van Tuan Mai ◽  
Xuan Chuong Tran
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Infection ◽  
Resistant Bacteria ◽  
Central Hospital ◽  
International Consensus ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Results Of Treatment ◽  
Amoxicillin Clavulanic Acid ◽  
Relationship Of

Sepsis is a serious bacterial infection. The main treatment is using antibiotics. However, the rate of antibiotic resistance is very high and this resistance is related to the outcome of treatment. Objectives: To evaluate the situation of antibiotic resistance of some isolated bacteria in sepsis patients treated at Hue Central Hospital; to evaluate the relationship of antibiotic resistance to the treatment results in patients with sepsis. Subjects and methods: prospective study of 60 sepsis patients diagnosed according to the criteria of the 3rd International Consensus-Sepsis 3 and its susceptibility patterns from April 2017 to August 2018. Results and Conclusions: The current agents of sepsis are mainly S. suis, Burkhoderiae spp. and E. coli. E. coli is resistant to cephalosporins 3rd, 4th generation and quinolone group is over 75%; resistance to imipenem 11.1%; the ESBL rate is 60%. S. suis resistant to ampicilline 11.1%; no resistance has been recorded to ceftriaxone and vancomycine. Resistance of Burkholderiae spp. to cefepime and amoxicillin/clavulanic acid was 42.9% and 55.6%, resistant to imipenem and meropenem is 20%, resistance to ceftazidime was not recorded. The deaths were mostly dued to E. coli and K. pneumoniae. The mortality for patients infected with antibiotic-resistant bacteria are higher than for sensitive groups. Key words: Sepsis, bacterial infection, antibiotics

scholarly journals Multiresistant Bacteria Isolated from Intestinal Faeces of Farm Animals in Austria

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 466
Author(s):  
Herbert Galler ◽  
Josefa Luxner ◽  
Christian Petternel ◽  
Franz F. Reinthaler ◽  
Juliana Habib ◽  
...  
Keyword(s):  
Meat Products ◽  
Animal Husbandry ◽  
Multidrug Resistant ◽  
Farm Animals ◽  
Resistant Bacteria ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Multiresistant Bacteria ◽  
Vancomycin Resistant

In recent years, antibiotic-resistant bacteria with an impact on human health, such as extended spectrum β-lactamase (ESBL)-containing Enterobacteriaceae, methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE), have become more common in food. This is due to the use of antibiotics in animal husbandry, which leads to the promotion of antibiotic resistance and thus also makes food a source of such resistant bacteria. Most studies dealing with this issue usually focus on the animals or processed food products to examine the antibiotic resistant bacteria. This study investigated the intestine as another main habitat besides the skin for multiresistant bacteria. For this purpose, faeces samples were taken directly from the intestines of swine (n = 71) and broiler (n = 100) during the slaughter process and analysed. All samples were from animals fed in Austria and slaughtered in Austrian slaughterhouses for food production. The samples were examined for the presence of ESBL-producing Enterobacteriaceae, MRSA, MRCoNS and VRE. The resistance genes of the isolated bacteria were detected and sequenced by PCR. Phenotypic ESBL-producing Escherichia coli could be isolated in 10% of broiler casings (10 out of 100) and 43.6% of swine casings (31 out of 71). In line with previous studies, the results of this study showed that CTX-M-1 was the dominant ESBL produced by E. coli from swine (n = 25, 83.3%) and SHV-12 from broilers (n = 13, 81.3%). Overall, the frequency of positive samples with multidrug-resistant bacteria was lower than in most comparable studies focusing on meat products.

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