Urine Tests for Diagnosis of Infectious Diseases and Antibiotic-Resistant Pathogens

The relation between disease and urine was recognized by physicians since the earliest civilization BC. Urine is considered an ideal diagnostic specimen for its noninvasive and easy method of collection. Urinalysis encompasses a wide range of tests, which includes a variety of chemical tests, urine microscopy, bacterial cultures, and molecular tests. Importantly, urine tests can diagnose patients with antibiotic-resistant urinary tract infections (UTI), directly from urine and/or bacterial culture. This chapter summarizes the most common urine tests in the infectious disease field, with a special focus on diagnosing UTI and characterizing their antibiotic resistant. In addition to describing the advantages and limitation of these tests, the chapter explores the promising emerging technologies and methods in this field. This chapter is beneficial for scientists and healthcare workers in the field

Colorimetric gold nanoparticles-based assay for direct detection of Clostridium difficile in clinical isolates from Qatar

Clostridium difficile infection (CDI) is a significant health problem worldwide. Control and prevention strategies of C. difficile horizontal transmission require assays with fast detection with high specificity and sensitivity. Conventional diagnostic methods are time consuming and costly for clinical field settings. This study aims to develop gold nanoparticles (AuNPs)-based assay for direct qualitative detection of the nucleic acid of C. difficile and its toxins. A colloidal solution of AuNPs with a diameter of 13±1 nm was prepared and characterized. The qualitative colorimetric AuNPs assay was developed for restricted genomic C. difficile DNA detection, and results were confirmed by PCR. One hundred and five positive C. difficile isolates were collected from patients with diarrheal diseases and tested using AuNPs based-assay. Ninety-six samples (91.4%) were detected positive using AuNPs based assay, as indicated by the color change from red to blue within 1 min. All ninety-six positive samples were positive for toxin B. In conclusion, nano-gold assay prototype was developed for direct and inexpensive detection of C. difficile. The developed prototypes are simple, sensitive, rapid and can substitute PCR-based detection. The developed assay may show potential in the clinical diagnosis of C. difficile, especially in developing countries as it is less costly as compared to the commercially available assays.NPRP award (NPRP 4-1215-3-317) from the Qatar National Research Fun

Microbiome engineering to combat antimicrobial resistance and upsurge productivity of food animals: a systematic review

Extensive antimicrobial usage in animal farming plays a prominent role in the antimicrobial resistance (AMR) crisis and is repeatedly highlighted as an area needing development under the ‘One Health’ approach. Alternative therapies such as microbiome products can be used as prophylaxis to help avoid infectious disease. However, a limited number of studies have focused on AMR-targeted microbiome products. We conducted this systematic review by using PRISMA guidelines to screen for literature that have evaluated food animals’ health when administrated with microbiome products targeting antimicrobial resistance (AMR) or antibiotic-resistant genes (ARGs). We searched and examined studies from SCOPUS, Web of Science, Embase, and Science direct databases for studies published up to November 2021, restricted to the English language. The findings of this review showed that microbiome products have a promising capability to tackle specific AMR/ARGs coupled with animal’s health and productivity improvement. Furthermore, our study showed that probiotics were the most favorable tested microbiome products, with the most targeted resistance being to tetracycline, macrolides, and beta-lactams. While microbiome products are promising alternatives to antibiotic prophylactics, there is a dearth of studies investigating their efficacy in targeting AMR. Thus, it is highly recommended to further investigate, develop, and improve the microbiome, to better understand its utility and circumvent its limitations.The authors thank Barzan holdings for the financial support

Antibacterial and Antibiofilm Activity of Mercaptophenol Functionalized-Gold Nanorods Against a Clinical Isolate of Methicillin-Resistant Staphylococcus aureus

Gold nanorods (AuNRs) were synthesized by the seed-mediated wet chemical method using a binary surfactant system. AuNRs were stabilized with polyethylene glycol, then functionalized with 4-mercaptophenol (4-MPH) ligand by surface ligand exchange. The surface-functionalized AuNRs (4-MPH-AuNRs) exhibited a typical UV–vis spectrum of AuNRs with a slightly shifted longitudinal peak. Furthermore, 4-MPH-AuNRs demonstrated a similar Fourier-Transformed Infrared spectrum to 4-MPH and a fading of the thiol band, which suggests a successful functionalization through thiol-gold binding. The antibacterial and antibiofilm activities of 4-MPH-AuNRs were evaluated against a clinical isolate of Methicillin-Resistant Staphylococcus aureus (MRSA). The results indicate that 4-MPH-AuNRs exhibit a bactericidal activity with a minimum inhibitory concentration (MIC) of ~ 6.25 μ g/mL against a planktonic suspension of MRSA. Furthermore, 4-MPH-AuNRs resulted in a 1.8–2.9 log-cycle reduction of MRSA biofilm viable count over a concentration range of 100–6.0 μ g/mL. The bacterial uptake of the surface-modified nanorods was investigated by inductively coupled plasma-optical emission spectroscopy (ICP-OES) and scanning electron microscopy (SEM) imaging; the results reveal that the nanorods were internalized into the bacterial cells after 6 h (h) of exposure. SEM imaging revealed a significant accumulation of the nanorods at the bacterial cell wall and a possible cellular internalization. Thus, 4-MPH-AuNRs can be considered a potential antibacterial agent, particularly against MRSA strain biofilms.Open Access funding provided by the Qatar National Library. Funding was provided by Al-Zaytoonah University of Jordan (2020-2019/12/28) and Qatar University (BRC-2021-ID-02, QUST-2-CHS-2021-2019)

Retail Chicken Carcasses as a Reservoir of Multidrug-Resistant .

is a major cause of foodborne disease outbreaks worldwide, mainly through poultry. Recently, there has been an increase in multidrug-resistant (MDR) infections globally. The increased drug resistance results in increased costs and poorer health outcomes due to unavailability or delayed treatment. This study aims to determine the prevalence of in retail raw chicken meat and identify their antimicrobial resistance profiles. A total of 270 retail raw chicken carcasses (local and imported) were collected from three hypermarket chains in Qatar between November 2017 and April 2018. Thirty carcasses were contaminated with (11.11%). The prevalence of in locally produced chicken was higher than in imported chicken (OR = 2.56, 95% CI: 1.18-5.53,  = 0.016). No significant differences were found between the prevalence and storage temperature or hypermarket chain. The highest resistance rates in the isolates were reported to tetracycline (73.7%) followed by nitrofurantoin (53.3%), ampicillin (50%), amoxicillin-clavulanic acid, ceftriaxone (26.7%), and ciprofloxacin (23.3%). Eight isolates were potential extended-spectrum β-lactamase-producers, all in imported frozen chicken ( < 0.0001). Additionally, 43.3% of the isolates were MDR and associated with frozen chicken (OR = 16.88, 95% CI: 2.55-111.47,  = 0.002). The findings indicate that while the prevalence of in retail chicken in Qatar is moderate, a large proportion of them are MDR.This research was funded by, Biomedical Research Centre, Qatar University, grant number “BRC-2018-ID-01 to Nahla O. Eltai.

The Spectrum of Antibiotic Prescribing During COVID-19 Pandemic: A Systematic Literature Review

Objectives: Over the last decades, there has been a significant increase in antimicrobial prescribing and consumption associated with the development of patients’ adverse events and antimicrobial resistance (AMR) to the point of becoming a global priority. This study aims at evaluating antibiotic prescribing during COVID- 19 pandemic from November 2019 to December 2020. Materials and Methods: A systematic review was conducted primarily through the NCBI database, using PRISMA guidelines to identify relevant literature for the period between November 1, 2019 and December 19, 2020, using the keywords: COVID-19 OR SARS-Cov-2 AND antibiotics restricted to the English language excluding nonclinical articles. Five hundred twenty-seven titles were identified; all articles fulfilling the study criteria were included, 133 through the NCBI, and 8 through Google Scholar with a combined total of 141 studies. The patient’s spectrum included all ages from neonates to elderly with all associated comorbidities, including immune suppression. Results: Of 28,093 patients included in the combined studies, 58.7% received antibiotics (16,490/28,093), ranging from 1.3% to 100% coverage. Antibiotics coverage was less in children (57%) than in adults with comorbidities (75%). Broad-spectrum antibiotics were prescribed presumptively without pathogen identifications, which might contribute to adverse outcomes. Conclusions: During the COVID-19 pandemic, there has been a significant and wide range of antibiotic prescribing in patients affected by the disease, particularly in adults with underlying comorbidities, despite the paucity of evidence of associated bacterial infections. The current practice might increase patients’ immediate and long-term risks of adverse events, susceptibility to secondary infections as well as aggravating AM

Whole genome-based genetic insights of blaNDM producing clinical E. coli isolates in hospitals settings of Pakistan

Carbapenem resistance among Enterobacterales has become a global health concern. Clinical Escherichia coli isolates producing the metallo β-lactamase NDM have been isolated from two hospitals in Faisalabad, Pakistan. These E. coli strains were characterized by MALDI-TOF, PCR, antimicrobial susceptibility testing, XbaI and S1 nuclease pulsed-field gel electrophoresis (PFGE), conjugation assay, DNA hybridization, whole genome sequencing, bioinformatic analysis, and Galleria mellonella experiments. Thirty-four blaNDM producing E. coli strains were identified among 52 nonduplicate carbapenem-resistant strains. More than 90% of the isolates were found to be multidrug resistant by antimicrobial susceptibility testing. S1 PFGE confirmed the presence of blaNDM gene on plasmids ranging from 40 kbps to 250 kbps, and conjugation assays demonstrated transfer frequencies of blaNDM harboring plasmids ranging from 1.59 × 10−1 to 6.46 × 10−8 per donor. Whole genome sequencing analysis revealed blaNDM-5 as the prominent NDM subtype with the highest prevalence of blaOXA-1, blaCTX-M-15, aadA2, aac(6')-Ib-cr, and tet(A) associated resistant determinants. E. coli sequence types: ST405, ST361, and ST167 were prominent, and plasmid Inc types: FII, FIA, FIB, FIC, X3, R, and Y, were observed among all isolates. The genetic environment of blaNDM region on IncF plasmids included partial ISAba125, the bleomycin ble gene, and a class I integron. The virulence genes terC, traT, gad, fyuA, irp2, capU, and sitA were frequently observed, and G. mellonella experiments showed that virulence correlated with the number of virulence determinants. A strong infection control management in the hospital is necessary to check the emergence of carbapenem resistance in Gram-negative bacteria. IMPORTANCE We describe a detailed analysis of highly resistant clinical E. coli isolates from two tertiary care centers in Pakistan including carbapenem resistance as well as common co-resistance mechanisms. South Asia has a huge problem with highly resistant E. coli. However, we find that though these isolates are very difficult to treat they are of low virulence. Thus the Western world has an increasing problem with virulent E. coli that are mostly of low antibiotic resistance, whereas, South Asia has an increasing problem with highly resistant E. coli that are of low virulence potential. These observations allow us to start to devise methodologies to limit both virulence and resistance and combat problems in developing nations as well as the Western world

Seroprevalence of camel brucellosis in Qatar

Brucellosis is a significant zoonotic disease and one of the most common neglected diseases worldwide. It can infect a wide range of domestic and wild animal species. Infected animals are usually culled, causing substantial economic losses to animal owners and the country’s economy in general. The disease is endemic among cattle, sheep, and goats in many countries around the Middle East and prevalent in most Gulf Cooperation Council countries, comprising a significant public health risk in the region. This study investigated the seroprevalence of brucellosis among camels in Qatar. Two hundred and forty-eight samples were collected from dromedary camels from 28 farms across the entire country. Each sample was tested for Brucella antibodies with both Rose Bengal and competitive enzyme-linked immunosorbent assay. Only samples that tested positive by both tests were considered seropositive for brucellosis. The overall prevalence was (20.6%, 95% CI, 15.7–26.1). The association between sex and seropositivity was slightly significant (Χ2 = 4.32, P = 0.04), with higher seroprevalence in females. Camels below breeding age (i.e., < 4 years old) showed decreased seropositivity (3.4%, 95% CI, 0.1–17.8), compared to (22.8%, 95% CI, 17.4–29.0) seropositivity in camels ≥ 4 years of age, with a significant association between age groups and seropositivity (P = 0.02). Our results indicate that the seroprevalence of brucellosis in Qatar’s camels is alarming, mandating more efforts to control the disease. The findings of this study will aid in selecting better effective measures to control camel brucellosis in Qatar. Further studies need to be conducted on Brucella infection among camels to determine the predisposing risk factors and the steps that should be followed to control brucellosis.Open Access funding provided by the Qatar National Library. This work was supported by Qatar University grant number QUCG-BRC-20/21–2 and high potential projects program QPH3P-BRC-2021–604 to Nahla O. Eltai

Assessment of Indoor Air Quality of Four Primary Health Care Centers in Qatar.

Airborne bacteria pose a potential risk to human health upon inhalation in the indoor environments of health care facilities. Airborne bacteria may originate from various sources, including patients, workers, and daily visitors. Hence, this study investigates the quantity, size, and identification of airborne bacteria indoors and outdoors of four Primary Health Care Centers (PHCC) in Doha, Qatar. Air samples were collected from the lobby, triage room, and outside environment of the centers, including, Qatar University (QU-HC), Al-Rayyan (AR-HC), Umm-Ghuwailina (UG-HC), and Old Airport (OA-HC) between August 2020 and March 2021, throughout both the hot and the cold seasons. Samples were collected using an Anderson six-stage cascade impactor. The mean of the total colony-forming units was calculated per cubic meter of air (CFU/m). QU-HC had the lowest mean of total bacterial count compared with other centers in the indoor and outdoor areas with 100.4 and 99.6 CFU/m, respectively. In contrast, AR-HC had the highest level, with 459 CFU/m indoors, while OA-HC recorded the highest bacterial concentration of the outdoor areas with a total mean 377 CFU/m. In addition, 16S rRNA sequencing was performed for genera identification. , , , and were the four most frequently identified bacterial genera in this study. The abundance of airborne bacteria in the four health centers was higher in the cold season. About 46% of the total airborne bacterial count for three PHCC centers exceeded 300 CFU/m, making them uncompliant with the World Health Organization's (WHO) recommendation for indoor settings. Consequently, an IAQ standards should be shaped to establish a baseline for measuring air pollution in Qatar. Additionally, it is crucial to understand seasonal fluctuations better so that hospitals can avoid rising and spreading infection peaks.This research was funded partially by Primary Health Care Corporation, grant number PHCC/RC/18/06/002

Profiling of intestinal microbiota in patients infected with respiratory influenza a and b viruses

Little is known about the association between respiratory viral infections and their impact on intestinal microbiota. Here, we compared the effect of influenza types, A and B, and influenza shedding in patients’ stools on the gut microbiota diversity and composition. Deep sequencing analysis was performed for the V4 region of the 16S rRNA gene. Fecal samples were collected from 38 adults with active respiratory influenza infection and 11 age-matched healthy controls. Influenza infection resulted in variations in intestinal bacterial community composition rather than in overall diversity. Overall, infected patients experienced an increased abundance of Bacteroidetes and a corresponding decrease in Firmicutes. Differential abundance testing illustrated that differences in gut microbiota composition were influenza type-dependent, identifying ten differentially abun-dant operational taxonomic units (OTUs) between influenza A-and influenza B-infected patients. Notably, virus shedding in fecal samples of some patients had significantly reduced gut bacterial diversity (p = 0.023). Further taxonomic analysis revealed that the abundance of Bacteroides fragilis was significantly higher among shedders compared to non-shedders (p = 0.037). These results pro-vide fundamental evidence of the direct effect of influenza infection on gut microbiota diversity, as reported in patients shedding the virus