Antibiotic Resistance
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2022 ◽  
Vol 168 ◽  
pp. 105372
Wanghong Su ◽  
Tongtong Li ◽  
Qiaoling Yu ◽  
Tianshu Feng ◽  
Jiawei Yang ◽  

Geoderma ◽  
2022 ◽  
Vol 411 ◽  
pp. 115698
Xue-Mei Han ◽  
Hang-Wei Hu ◽  
Jin-Yang Li ◽  
He-Lian Li ◽  
Fang He ◽  

2022 ◽  
Vol 160 ◽  
pp. 107077
Joan Cáliz ◽  
Jèssica Subirats ◽  
Xavier Triadó-Margarit ◽  
Carles M. Borrego ◽  
Emilio O. Casamayor

2022 ◽  
Vol 17 (1) ◽  
Paul Jankowski ◽  
Jaydon Gan ◽  
Tri Le ◽  
Michaela McKennitt ◽  
Audrey Garcia ◽  

Abstract Background Wastewater treatment plants are an essential part of maintaining the health and safety of the general public. However, they are also an anthropogenic source of antibiotic resistance genes. In this study, we characterized the resistome, the distribution of classes 1–3 integron-integrase genes (intI1, intI2, and intI3) as mobile genetic element biomarkers, and the bacterial and phage community compositions in the North End Sewage Treatment Plant in Winnipeg, Manitoba. Samples were collected from raw sewage, returned activated sludge, final effluent, and dewatered sludge. A total of 28 bacterial and viral metagenomes were sequenced over two seasons, fall and winter. Integron-integrase genes, the 16S rRNA gene, and the coliform beta-glucuronidase gene were also quantified during this time period. Results Bacterial classes observed above 1% relative abundance in all treatments were Actinobacteria (39.24% ± 0.25%), Beta-proteobacteria (23.99% ± 0.16%), Gamma-proteobacteria (11.06% ± 0.09%), and Alpha-proteobacteria (9.18 ± 0.04%). Families within the Caudovirales order: Siphoviridae (48.69% ± 0.10%), Podoviridae (23.99% ± 0.07%), and Myoviridae (19.94% ± 0.09%) were the dominant phage observed throughout the NESTP. The most abundant bacterial genera (in terms of average percent relative abundance) in influent, returned activated sludge, final effluent, and sludge, respectively, includes Mycobacterium (37.4%, 18.3%, 46.1%, and 7.7%), Acidovorax (8.9%, 10.8%, 5.4%, and 1.3%), and Polaromonas (2.5%, 3.3%, 1.4%, and 0.4%). The most abundant class of antibiotic resistance in bacterial samples was tetracycline resistance (17.86% ± 0.03%) followed by peptide antibiotics (14.24% ± 0.03%), and macrolides (10.63% ± 0.02%). Similarly, the phage samples contained a higher prevalence of macrolide (30.12% ± 0.30%), peptide antibiotic (10.78% ± 0.13%), and tetracycline (8.69% ± 0.11%) resistance. In addition, intI1 was the most abundant integron-integrase gene throughout treatment (1.14 × 104 gene copies/mL) followed by intI3 (4.97 × 103 gene copies/mL) while intI2 abundance remained low (6.4 × 101 gene copies/mL). Conclusions Wastewater treatment successfully reduced the abundance of bacteria, DNA phage and antibiotic resistance genes although many antibiotic resistance genes remained in effluent and biosolids. The presence of integron-integrase genes throughout treatment and in effluent suggests that antibiotic resistance genes could be actively disseminating resistance between both environmental and pathogenic bacteria.

2022 ◽  
Emily F Wissel ◽  
Brooke M Talbot ◽  
Bjorn A Johnson ◽  
Robert A Petit ◽  
Vicki Hertzberg ◽  

The use of shotgun metagenomics for AMR detection is appealing because data can be generated from clinical samples with minimal processing. Detecting antimicrobial resistance (AMR) in clinical genomic data is an important epidemiological task, yet a complex bioinformatic process. Many software tools exist to detect AMR genes, but they have mostly been tested in their detection of genotypic resistance in individual bacterial strains. It is important to understand how well these bioinformatic tools detect AMR genes in shotgun metagenomic data. We developed a software pipeline, hAMRoaster (, for assessing accuracy of prediction of antibiotic resistance phenotypes. For evaluation purposes, we simulated a short read (Illumina) shotgun metagenomics community of eight bacterial pathogens with extensive antibiotic susceptibility testing profiles. We benchmarked nine open source bioinformatics tools for detecting AMR genes that 1) were conda or Docker installable, 2) had been actively maintained, 3) had an open source license, and 4) took FASTA or FASTQ files as input. Several metrics were calculated for each tool including sensitivity, specificity, and F1 at three coverage levels. This study revealed that tools were highly variable in sensitivity (0.25 - 0.99) and specificity (0.2 - 1) in detection of resistance in our synthetic FASTQ files despite similar databases and methods implemented. Tools performed similarly at all coverage levels (5x, 50x, 100x). Cohen’s kappa revealed low agreement across tools.

Siham Ali Hizam Al-Arosi ◽  
Essam Yahiya Al-shamahi ◽  
Abdulwahab Ismail Mohamed Al-Kholani ◽  
Ahmed Yahiya Al-Jawfi ◽  
Hassan Abdulwahab Al-Shamahy ◽  

Background: Ophthalmia neonatorum (ON) is the most widespread eye infection occurring in the first 28 days of life. Although most of these cases are benign, some may progress to systemic complications or blindness if left untreated. Objectives: The current study was conducted with the aim of revealing the bacteriological causes of conjunctivitis in neonates and the antibiotic sensitivity pattern of these bacteria. Subjects and methods: The study included all neonates at the age of 1 to 28 days presenting at the neonatal nurseries with Neonatal Intensive Care Unit (NICU) and level II care beds in three hospitals; Authority of Al-Thawra General Hospital, Al-Kuwait University Hospital and Al-Sabeen Maternity and Child Hospital in Sana’a city, Yemen. A full history was taken from each nurse and mothers of the neonates included in the study in which the findings were recorded in a predesigned questionnaire including socio demographic, maternal clinical information and therapeutic interventions. To isolate the causative agent, the conjunctival swabs were inoculated on proper media and bacteria were identified by standard microbiological methods and antibiotic resistance was done for the isolates. Results: 203 swabs were collected from newborns with eye discharge over a nine-month period. Positive growth rate was 51.7%, males were more affected (57.1%), 80% of affected neonates had low birth weight, 71.4% of preterm infants were most affected (p <0.01).  There was a significant relationship between invasive and non-invasive mechanical ventilation with neonatal conjunctivitis (p<0.05). Gentamicin showed good in vitro sensitivity to all bacteria isolated, Staphylococcus aureus (83%), Escherichia coli 84.6%, with P. aeruginosa it was 60%. Conclusion: The vast majority of cases of neonatal conjunctivitis were mild with a high level of occurrence, Staphylococcus aureus and Klebsiella pneumoniae were the major bacterial agents, neonatal conjunctivitis most likely to be a hospital-acquired infection. There was a significant association between phototherapy, non-invasive ventilation and incidence of neonatal conjunctivitis . Gentamicin had high activity against the bacteria isolated in this study.                   Peer Review History: Received: 9 November 2021; Revised: 11 December; Accepted: 27 December, Available online: 15 January 2022 Academic Editor: Dr. Sally A. El-Zahaby, Pharos University in Alexandria, Egypt, [email protected] UJPR follows the most transparent and toughest ‘Advanced OPEN peer review’ system. The identity of the authors and, reviewers will be known to each other. This transparent process will help to eradicate any possible malicious/purposeful interference by any person (publishing staff, reviewer, editor, author, etc) during peer review. As a result of this unique system, all reviewers will get their due recognition and respect, once their names are published in the papers. We expect that, by publishing peer review reports with published papers, will be helpful to many authors for drafting their article according to the specifications. Auhors will remove any error of their article and they will improve their article(s) according to the previous reports displayed with published article(s). The main purpose of it is ‘to improve the quality of a candidate manuscript’. Our reviewers check the ‘strength and weakness of a manuscript honestly’. There will increase in the perfection, and transparency.  Received file:                Reviewer's Comments: Average Peer review marks at initial stage: 6.0/10 Average Peer review marks at publication stage: 7.0/10 Reviewers: Dr. Bilge Ahsen KARA, Ankara Gazi Mustafa Kemal Hospital, Turkey, [email protected] Dr. Jucimary Vieira dos Santos, Hemonorte Dalton Barbosa Cunha, Brazil, [email protected]  Similar Articles: BACTERIAL CONJUNCTIVITIS OF ADULTS: CAUSES AND OPHTHALMIC ANTIBIOTIC RESISTANCE PATTERNS FOR THE COMMON BACTERIAL ISOLATES BACTERIAL CAUSES AND ANTIMICROBIAL SENSITIVITY PATTERN OF EXTERNAL OCULAR INFECTIONS IN SELECTED OPHTHALMOLOGY CLINICS IN SANA’A CITY

Pathogens ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 91
Kevin Maclean ◽  
Fernande Olpa J Pankendem Njamo ◽  
Mahloro Hope Serepa-Dlamini ◽  
Kulsum Kondiah ◽  
Ezekiel Green

SCUBA divers are predisposed to otitis externa caused by Pseudomonas aeruginosa, which is becoming increasingly multi-drug resistant (MDR). The present work assessed the antibiotic resistance profiles of P. aeruginosa obtained from SCUBA divers and their environment in Sodwana Bay, South Africa. Bacterial isolates from a total of 137 random water and ear swab samples were identified using biochemical and molecular methods. P. aeruginosa strains were further evaluated for antibiotic susceptibility using the Kirby–Bauer assay. Double disk synergy test (DDST) to confirm metallo-β-lactamase (MBL) production and PCR amplification of specific antibiotic resistance genes was performed. All (100%) 22 P. aeruginosa isolates recovered were resistant to 6 of the β-lactams tested including imipenem but exhibited susceptibility to trimethoprim–sulfamethoxazole. MBL production was observed in 77% of isolates while the most prevalent extended-spectrum β-lactamase (ESBL) genes present included blaAmpC (86.9%) followed by blaTEM (82.6%). Sulfonamide resistance was largely encoded by sul1 (63.6%) and sul2 (77.3%) genes with a high abundance of class 1 integrons (77.3%) of which 18.2% carried both Intl1 and Intl2. P. aeruginosa found in Sodwana Bay exhibits multi-drug resistance (MDRce) to several pharmaceutically important drugs with the potential to transfer antibiotic resistance to other bacteria if the judicious use of antibiotics for their treatment is not practiced.

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