**Abstract**

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.

**Keywords:** urine, infectious diseases, urinalysis, bacteria, antibiotic resistance

#### **1. Introduction**

Urinalysis has been a useful diagnostic tool since thousands of years. Although urine was the first body fluid to be examined by mankind for the diagnosis of diseases [1], it is still one of the most common specimens used in clinical and diagnostic laboratories. Urine samples have been used for the diagnosis of a wide and diverse range of disorders, including but not limited to renal diseases [2, 3], metabolic disorders [4], cancer [5], infectious diseases [6], and others [7–10].

In infectious disease field, urine tests are applied in diagnosing urinary tract infections (UTI) [11–13]. Further, several other infections can be diagnosed by urine tests at different levels [14] including community-acquired pneumonia (CAP) [15], legionellosis [16], tuberculosis [17, 18], congenital cytomegalovirus (CMV) infection [19], and dengue virus [20, 21], and recently, several papers suggest the high value of urinalysis in the detection of Zika virus [22, 23]. Parasites can also be diagnosed from the urine by detection of urinary egg, for example, diagnosis of *Schistosoma haematobium* (*S. haematobium)* [24]. Furthermore, urine has been used for screening of different sexually transmitted diseases (STD) such as *Neisseria gonorrhoeae* and *Chlamydia* sp. [25, 26]. The sensitivity and accuracy of urine test vary according to the agent being detected [14], and in some cases, urinalysis is only performed to exclude other diseases [27].

Many of the aforementioned infections are treated with antimicrobial drugs [28–30], a discovery of the past century that completely changed the medical field and saved millions of lives [31]. Unfortunately, this discovery did not last unchallenged for long; soon after the discovery of penicillin by Sir Alexander Fleming in 1928 [32], the problem of penicillin resistance first emerged in 1947—19 years after its discovery and 4 years after the dug started being mass-produced and was used heavily to treat allied troops fighting in Europe during the World War II. Ever since, antimicrobial resistance (AMR) has become a fierce challenge endangering the existence of many antimicrobial agents [33].

With the emergence of pathogenic strains resistant to almost all available antimicrobial drugs [34, 35] and with only few new drugs in the development and production pipeline [36], AMR is now one of the most urgent global health threats [33]. This emphasizes on the importance of urine analysis and detection of antimicrobial resistance in the diagnostic laboratories.

Treatment of UTI is a good example of AMR impact on the medical field. Many of the antibiotics prescribed traditionally for the treatment of UTIs are now compromised and to a large extent are ineffective [37]. More alarming, recent years have recorded the emergence of bacterial strains that are resistant to even last resort antibiotics such as colistin, making the treatment of UTIs a global challenge [38].
