scholarly journals A New Pipeline for Designing Phage Cocktails Based on Phage-Bacteria Infection Networks

2021 ◽  
Vol 12 ◽  
Author(s):  
Felipe Molina ◽  
Alfredo Simancas ◽  
Manuel Ramírez ◽  
Rafael Tabla ◽  
Isidro Roa ◽  
...  
Keyword(s):  
Host Range ◽  
Meta Analysis ◽  
Bacterial Load ◽  
Substantial Reduction ◽  
Raw Milk ◽  
Resistant Bacteria ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Raw Milk Cheese ◽  
Number Of Bacteria

In recent years, the spread of antibiotic-resistant bacteria and efforts to preserve food microbiota have induced renewed interest in phage therapy. Phage cocktails, instead of a single phage, are commonly used as antibacterial agents since the hosts are unlikely to become resistant to several phages simultaneously. While the spectrum of activity might increase with cocktail complexity, excessive phages could produce side effects, such as the horizontal transfer of genes that augment the fitness of host strains, dysbiosis or high manufacturing costs. Therefore, cocktail formulation represents a compromise between achieving substantial reduction in the bacterial loads and restricting its complexity. Despite the abovementioned points, the observed bacterial load reduction does not increase significantly with the size of phage cocktails, indicating the requirement for a systematic approach to their design. In this work, the information provided by host range matrices was analyzed after building phage-bacteria infection networks (PBINs). To this end, we conducted a meta-analysis of 35 host range matrices, including recently published studies and new datasets comprising Escherichia coli strains isolated during ripening of artisanal raw milk cheese and virulent coliphages from ewes’ feces. The nestedness temperature, which reflects the host range hierarchy of the phages, was determined from bipartite host range matrices using heuristic (Nestedness Temperature Calculator) and genetic (BinMatNest) algorithms. The latter optimizes matrix packing, leading to lower temperatures, i.e., it simplifies the identification of the phages with the broadest host range. The structure of infection networks suggests that generalist phages (and not specialist phages) tend to succeed in infecting less susceptible bacteria. A new metric (Φ), which considers some properties of the host range matrices (fill, temperature, and number of bacteria), is proposed as an estimator of phage cocktail size. To identify the best candidates, agglomerative hierarchical clustering using Ward’s method was implemented. Finally, a cocktail was formulated for the biocontrol of cheese-isolated E. coli, reducing bacterial counts by five orders of magnitude.

scholarly journals Diversity and Local Coadaptation of Escherichia coli and Coliphages From Small Ruminants

2020 ◽  
Vol 11 ◽  
Author(s):  
Felipe Molina ◽  
Alfredo Simancas ◽  
Rafael Tabla ◽  
Antonia Gómez ◽  
Isidro Roa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Host Range ◽  
Raw Milk ◽  
Coliform Bacteria ◽  
Cell Protein ◽  
Broad Host Range ◽  
High Positive Correlation ◽  
E Coli ◽  
Raw Milk Cheese

Bacteriophages are highly specific predators that drive bacterial diversity through coevolution while striking tradeoffs among preserving host populations for long-term exploitation and increasing their virulence, structural stability, or host range. Escherichia coli and other coliform bacteria present in the microbiota of milk and during early ripening of raw milk cheeses have been linked to the production of gas, manifested by the appearance of eyes, and the development of off-flavors; thus, they might cause early blowing and cheese spoilage. Here, we report the characterization of coliphages isolated from manure from small ruminant farms and E. coli strains isolated from goat and sheep raw milk cheese. Additionally, the virulence and host range of locally isolated and laboratory collection phages were determined by comparing the susceptibility of E. coli strains from different sources. In agreement with the high genetic diversity found within the species E. coli, clustering analysis of whole-cell protein revealed a total of 13 distinct profiles but none of the raw milk cheese isolates showed inhibition of growth by reference or water-isolated coliphages. Conversely, 10 newly isolated phages had a broad host range (i.e., able to lyse ≥50% of bacterial hosts tested), thus exhibiting utility for biocontrol and only one cheese-isolated E. coli strain was resistant to all the phages. Whereas there was a high positive correlation between bacterial susceptibility range and lysis intensity, the phages virulence decreased as range increased until reaching a plateau. These results suggest local gene-for-gene coevolution between hosts and phages with selective tradeoffs for both resistance and competitive ability of the bacteria and host-range extension and virulence of the phage populations. Hence, different phage cocktail formulations might be required when devising long-term and short-term biocontrol strategies.

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.

scholarly journals Prevalence and Characterization of Extended-Spectrum β-Lactamase-Producing Antibiotic-Resistant Escherichia coli and Klebsiella pneumoniae in Ready-to-Eat Street Foods

Antibiotics ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 850
Author(s):  
Shobha Giri ◽  
Vaishnavi Kudva ◽  
Kalidas Shetty ◽  
Veena Shetty
Keyword(s):  
Escherichia Coli ◽  
Food Safety ◽  
Klebsiella Pneumoniae ◽  
Rural Areas ◽  
Significant Risk ◽  
Microbiological Quality ◽  
Resistant Bacteria ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Extended Spectrum

As the global urban populations increase with rapid migration from rural areas, ready-to-eat (RTE) street foods are posing food safety challenges where street foods are prepared with less structured food safety guidelines in small and roadside outlets. The increased presence of extended-spectrum-β-lactamase (ESBL) producing bacteria in street foods is a significant risk for human health because of its epidemiological significance. Escherichia coli and Klebsiella pneumoniae have become important and dangerous foodborne pathogens globally for their relevance to antibiotic resistance. The present study was undertaken to evaluate the potential burden of antibiotic-resistant E. coli and K. pneumoniae contaminating RTE street foods and to assess the microbiological quality of foods in a typical emerging and growing urban suburb of India where RTE street foods are rapidly establishing with public health implications. A total of 100 RTE food samples were collected of which, 22.88% were E. coli and 27.12% K. pneumoniae. The prevalence of ESBL-producing E. coli and K. pneumoniae was 25.42%, isolated mostly from chutneys, salads, paani puri, and chicken. Antimicrobial resistance was observed towards cefepime (72.9%), imipenem (55.9%), cefotaxime (52.5%), and meropenem (16.9%) with 86.44% of the isolates with MAR index above 0.22. Among β-lactamase encoding genes, blaTEM (40.68%) was the most prevalent followed by blaCTX (32.20%) and blaSHV (10.17%). blaNDM gene was detected in 20.34% of the isolates. This study indicated that contaminated RTE street foods present health risks to consumers and there is a high potential of transferring multi-drug-resistant bacteria from foods to humans and from person to person as pathogens or as commensal residents of the human gut leading to challenges for subsequent therapeutic treatments.

scholarly journals Persulfate mediated solar photo-Fenton aiming at wastewater treatment plant effluent improvement at neutral PH: emerging contaminant removal, disinfection, and elimination of antibiotic-resistant bacteria

2021 ◽  
Author(s):  
Maria Clara V. M. Starling ◽  
Elizângela P. Costa ◽  
Felipe A. Souza ◽  
Elayne C. Machado ◽  
Juliana Calábria de Araujo ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Wastewater Treatment Plant ◽  
Treatment Plant ◽  
Resistant Bacteria ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Effluent Quality ◽  
Neutral Ph ◽  
Wastewater Treatment Plant Effluent

AbstractThis work investigated an innovative alternative to improve municipal wastewater treatment plant effluent (MWWTP effluent) quality aiming at the removal of contaminants of emerging concern (caffeine, carbendazim, and losartan potassium), and antibiotic-resistant bacteria (ARB), as well as disinfection (E. coli). Persulfate was used as an alternative oxidant in the solar photo-Fenton process (solar/Fe/S2O82−) due to its greater stability in the presence of matrix components. The efficiency of solar/Fe/S2O82− at neutral pH using intermittent iron additions is unprecedented in the literature. At first, solar/Fe/S2O82− was performed in a solar simulator (30 W m−2) leading to more than 60% removal of CECs, and the intermittent iron addition strategy was proved effective. Then, solar/Fe/S2O82− and solar/Fe/H2O2 were compared in semi-pilot scale in a raceway pond reactor (RPR) and a cost analysis was performed. Solar/Fe/S2O82− showed higher efficiencies of removal of target CECs (55%), E. coli (3 log units), and ARB (3 to 4 log units) within 1.9 kJ L−1 of accumulated irradiation compared to solar/Fe/H2O2 (CECs, 49%; E. coli, 2 log units; ARB, 1 to 3 log units in 2.5 kJ L−1). None of the treatments generated acute toxicity upon Allivibrio fischeri. Lower total cost was obtained using S2O82− (0.6 € m−3) compared to H2O2 (1.2 € m−3). Therefore, the iron intermittent addition aligned to the use of persulfate is suitable for MWWTP effluent quality improvement at neutral pH.

scholarly journals Prevalence of Mastitis and Antibiotic Resistance of Bacterial Isolates from CMT Positive Milk Samples Obtained from Dairy Cows, Camels, and Goats in Two Pastoral Districts in Southern Ethiopia

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1530
Author(s):  
Amanuel Balemi ◽  
Balako Gumi ◽  
Kebede Amenu ◽  
Sisay Girma ◽  
Muuz Gebru ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Dairy Cows ◽  
Raw Milk ◽  
Multidrug Resistant ◽  
Southern Ethiopia ◽  
Resistant Bacteria ◽  
Coagulase Negative Staphylococcus ◽  
Bacterial Isolates ◽  
E Coli ◽  
Milk Samples

A study was carried out from August 2017 to February 2018 on lactating dairy cows, one-humped dromedary camels, and goats to determine mastitis in the Bule Hora and Dugda Dawa districts of in Southern Ethiopia. Milk samples from 564 udder quarters and udder halves from 171 animals consisting of 60 dairy cows, 51 camels, and 60 goats were tested for mastitis. Sixty-four positive udder milk samples were cultured, and bacterial mastitis pathogens were isolated and identified. The antibiotic resistance of bacterial isolates from milk with mastitis was tested against nine antimicrobials commonly used in the study area. Cow- and quarter-level prevalence of mastitis in dairy cows, camels, and goats was 33.3%, 26.3%, and 25% and 17.6%, 14.5%, and 20%, respectively. In cattle, the prevalence was significantly higher in Dugda Dawa than in Bule Hora. Major bacterial isolates were coagulase-negative Staphylococcus species (39.1%), S. aureus (17.2%), S. hyicus (14.1%), and S. intermedius and Escherichia coli (9.4% each). In camels, udder abnormality and mastitis were significantly higher in late lactation than in early lactation. Mastitis tends to increase with parity in camels. E. coli isolates were highly resistant to spectinomycin, vancomycin, and doxycycline, whereas most S. aureus isolates were multidrug-resistant. Most of the rural and periurban communities in this area consume raw milk, which indicates a high risk of infection with multidrug-resistant bacteria. We recommend a community-focused training program to improve community awareness of the need to boil milk and the risk of raw milk consumption.

scholarly journals Occurrence of toxigenic Escherichia coli in raw milk cheese in Brazil

2007 ◽  
Vol 59 (2) ◽  
pp. 508-512 ◽  
Author(s):  
B.R. Paneto ◽  
R.P. Schocken-Iturrino ◽  
C. Macedo ◽  
E. Santo ◽  
J.M. Marin
Keyword(s):  
Escherichia Coli ◽  
Polymerase Chain Reaction ◽  
Antimicrobial Agents ◽  
Raw Milk ◽  
Diffusion Method ◽  
Chain Reaction ◽  
Disk Diffusion Method ◽  
E Coli ◽  
Polymerase Chain ◽  
Raw Milk Cheese

The occurrence of toxigenic Escherichia coli in raw milk cheese was surveyed in Middle Western Brazil. Fifty samples of cheese from different supermarkets were analyzed for E.coli. The isolates were serotyped and screened for the presence of verotoxigenic E. coli (VTEC) and enterotoxigenic E. coli (ETEC) by Polymerase Chain Reaction (PCR). The susceptibility to thirteen antimicrobial agents was evaluated by the disk diffusion method. E.coli were recovered from 48 (96.0%) of the samples. The serogroups identified were O125 (6.0%), O111 (4.0%), O55 (2.0%) and O119 (2.0%). Three (6.0%) and 1(2.0%) of the E.coli isolates were VTEC and ETEC, respectively. Most frequent resistance was observed to the following antimicrobials: cephalothin (60.0%), nalidixic acid (40.0%), doxycyclin (33.0%), tetracycline (31.0%) and ampicillin (29.0%).

scholarly journals Retail Chicken Carcasses as a Reservoir of Antimicrobial- Resistant Escherichia coli

2020 ◽  
Author(s):  
Nahla Omer Eltai ◽  
Hadi M. Yassine ◽  
Sara H. Al-Hadidi ◽  
Tahra ElObied ◽  
Asmaa A. Al Thani ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Growth Promotion ◽  
Multidrug Resistant ◽  
Chicken Meat ◽  
Resistant Bacteria ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Inappropriate Use ◽  
Esbl Producers

The dissemination of antimicrobial resistance (AMR) bacteria has been associated with the inappropriate use of antibiotics in both humans and animals and with the consumption of food contaminated with resistant bacteria. In particular, the use of antibiotics as prophylactic and growth promotion purposes in food-producing animals has rendered many of the antibiotics ineffective. The increased global prevalence of AMR poses a significant threat to the safety of the world’s food supply. Objectives: This study aims at determining the prevalence of antibiotic-resistant Escherichia coli (E. coli) isolated from local and imported retail chicken meat in Qatar. Methodology: A total of 270 whole chicken carcasses were obtained from three different hypermarket stores in Qatar. A total of 216 E. coli were isolated and subjected to antibiotic susceptibility testing against 18 relevant antibiotics using disc diffusion and micro- dilution methods. Furthermore, extended-spectrum β-lactamase (ESBL) production was determined via a double-disc synergetic test. Isolates harboring colistin resistance were confirmed using multiplex-PCR and DNA sequencing. Results: Nearly 89% (192/216) of the isolates were resistant to at least one antibiotics. In general, isolates showed relatively higher resistance to sulfamethoxazole (62%), tetracycline (59.7%), ampicillin and trimethoprim (52.3%), ciprofloxacin (47.7%), cephalothin, and colistin (31.9%). On the other hand, less resistance was recorded against amoxicillin/clavulanic acid (6%), ceftriaxone (5.1%), nitrofurantoin (4.2%) and piperacillin/tazobactam (4.2%), cefepime (2.3%), meropenem (1.4%), ertapenem (0.9%), and amikacin (0.9%). Nine isolates (4.2%) were ESBL producers. Furthermore, 63.4% were multidrug-resistant (MDR). The percentage of MDR, ESBL producers, and colistin-resistant isolates was significantly higher among local isolates compared to imported chicken samples. Conclusion: We reported a remarkably high percentage of the antibiotic-resistant E. coli in chicken meat sold at retail in Qatar. The high percentage of MDR and colistin isolates is troublesome to the food safety of raw chicken meat and the potential of antibiotic resistance spread to public health. Our findings support the need for the implementation of one health approach to address the spread of antimicrobial resistance and the need for a collaborative solution.

scholarly journals Isolation, characterization and efficacy of lytic bacteriophages against pathogenic Escherichia coli from hospital liquid waste

2020 ◽  
Vol 21 (7) ◽  
Author(s):  
Rahmad Lingga ◽  
Sri Budiarti ◽  
Iman Rusmana ◽  
Aris Tri Wahyudi
Keyword(s):  
Escherichia Coli ◽  
Host Range ◽  
Liquid Waste ◽  
Resistant Bacteria ◽  
Lytic Bacteriophage ◽  
Hospital Wastewater ◽  
Electron Micrograph ◽  
E Coli ◽  
Pathogenic Escherichia Coli ◽  
Phage Treatment

Abstract. Lingga R, Budiarti S, Rusmana I, Wahyu AT. 2020. Isolation, characterization and efficacy of lytic bacteriophages against pathogenic Escherichia coli from hospital liquid waste. Biodiversitas 21: 3234-3241. Escherichia coli is known as a pathogenic contaminant bacteria in hospital wastewater hazardous to humans and the environment. Concerns about the emergence of chlorine- and antibiotic-resistant bacteria increase the urgency to find an alternative strategy to control pathogenic bacteria in hospital wastewater. One of the alternatives is using lytic bacteriophage. This study aimed to isolate, characterize, and examine the efficacy of lytic bacteriophage against pathogenic Escherichia coli from hospital wastewater. It isolated, characterized (plaque morphology, host range, virion electron micrograph, and sensitivity to temperature, pH, and chlorine treatments), and tested the efficacy of lytic bacteriophages in controlling pathogenic E. coli isolated from hospital wastewater. Five phages were successfully obtained, all of which had clear plaques (lytic phage character). Based on host range assay, most of the phages could lyse all tested E. coli strains but not for other species. Electron micrograph photography revealed that the phages belonged to Myoviridae. The phages showed stability in high temperature, broad-ranged pH, and high concentrations of chlorine treatments. Assay on phages efficacy suggested that the phages are capable of significantly reducing the E. coli population both in sterilized and non-sterilized wastewater. The combination of phage treatment and chlorine was more effective than single phage treatment. The efficacy test revealed that phage application in wastewater had the best result seen from cocktail treatment and a combination of phage treatment and chlorine. These results suggested that the phage can be a potential candidate for disinfection purposes.

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