*2.1.2 Sample processing*

*Pathogenic Bacteria*

existence of many antimicrobial agents [33].

crobial resistance in the diagnostic laboratories.

can also be diagnosed with the help of urinalysis.

*coli* representing about 40–70% of the cases [27].

the patient, with latter being the most essential element [27].

**2.1 Urinalysis for diagnosis of urinary tract infection**

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

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 antimi-

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].

A urine specimen is one of the most frequent specimens examined in many of the clinical- and hospital-based laboratories. Urine cultures account for up to 40% of those laboratories' cultures, making it the most common type of culture in such laboratories [27]. Urine is considered an ideal diagnostic specimen for its noninvasive, easy method of collection and the sufficient amount in which it is excreted [14]. The most common infections diagnosed by urinalysis are UTIs, which are one of the most common bacterial infections that require medical intervention. Several other infections such as community-acquired pneumonia and viremia infections

UTI affects about 150 million around the globe every year [28]. Urinary tract infections are common in women and to less extent in children. Many women experience multiple infections during their lifetimes. Risk factors specific to women for UTIs include female anatomy. A woman has a shorter urethra than a man does, which shortens the distance that bacteria must travel to reach the bladder [39]. UTIs are generally categorized clinically as complicated and uncomplicated based on the presence of risk factors that comprise the urinary tract or the host defense [40]. Both Gram-negative and Gram-positive bacteria can cause UTIs, with *Escherichia* 

The diagnosis of UTIs is mainly based on urinalysis and the medical history of

Avoiding contamination is a key element when collecting samples for diagnostic purposes. Bacterial contamination of the urine during collection is always a concern, and midstream urine is recommended for UTI. Clear instruction to the patient is indicated to reduce the risk of contamination with the use of clean containers.

**2. Urine tests for infectious disease diagnostics and treatment**

**188**

*2.1.1 Sample collection*

The clinical information obtained from a urine specimen is influenced by the collection method, timing, and handling. An enormous variety of collection and transport containers for urine specimens are available, depending on the type of laboratory test ordered. National Committee for Clinical Laboratory Standards (NCCLS) recommended testing urine sample within 2 hours of collection to avoid false-positive results; however refrigeration or chemical preservation of urine specimens may be utilized if testing or refrigeration within a two-hour window is not possible. A variety of urine preservatives (tartaric and boric acids being the most common) are available that allow urine to be kept at room temperature while still providing results comparable to those of refrigerated urine. Generally, the length of preservation capacity ranges from 24 to 72 hours. Metabolites which can be significantly influenced by the interaction of exposure time and temperature include arginine, glutamine, methionine, phenylalanine, and others, while metabolites which can be significantly influenced by freeze and thaw cycles are the C3 family and histones H1 [44].

### *2.1.3 Urine microscopy*

Bacteria can be simply observed in urine specimens under the microscope, especially after Gram staining. After centrifugation of urine samples, a small amount of the pellet is applied to a glass microscopic slide and stained with the usual Gram-staining protocol. Gram staining can also be done to uncentrifuged specimen; however, there are no definitive criteria to determine positive results with this method, and it is not sensitive for detection of low number of bacteria.

Although Gram-staining test can give relatively fast results about the nature of the causative agent; however it is not practical for routine use, it is labor intensive, insensitive test for concentration of bacteria lower than 105 cfu/mL, and timeconsuming, making it unsuitable for the patient with uncomplicated UTIs [45]*.*

#### *2.1.4 Urine nitrite test*

*Enterobacteriaceae* are the main causative agent of UTI. They typically produce nitrite, thus making this bacterium chemically detectable. The urine sample for this test should be taken from the first urine produced in the morning, as a minimum of 4 hours are required for the bacteria to produce a detectable amount nitrite. Unfortunately, other bacteria such *as Staphylococcus saprophyticus* cannot produce nitrite, introducing limitation for this test [46].

#### *2.1.5 Pyuria*

The presence of pus in the urine (i.e., pyuria) can be detected by various methods. The best and most accurate method is to microscopically measure the urinary leukocyte excretion rate. Other microscopic methods may also include counting the leukocyte in the urine. However, as the microscopic method is unpractical for routine use, other easier methods such as leukocyte esterase tests for detection of pyuria can be performed. The leukocyte esterase tests have many disadvantages as it produces false-positive results due the presence of eosinophils in the urine. Decreased positive results or false-negative results of this test are referred to other reasons including elevated level of glucose and protein in the urine or if the patient is treated with certain drugs such as cephalexin or tetracycline [47]. The commercial products are believed to be more efficient, although they have low sensitivity, but they are highly specific, and they provide information about both pyuria and bacteriuria [27].

## *2.1.6 Urine culture*

Urine culture is the gold standard in diagnosing UTI. It is crucial not only for the diagnosis but also to guide appropriate antimicrobial prescription and treatment. Patients with complicated UTIs, those who have suffered from recurrent UTIs, or those who are not responding to the empirical treatment are the ones usually subjected for urine culture. In this regard, the most common used culture media are the blood agar and MacConkey's agar. This is especially true for specimen from outpatients, knowing that almost all UTIs in outpatients are caused by aerobic and facultative Gram-negative bacteria, making it unnecessary to use a medium that is selective for Gram-positive bacteria. However, for the hospitalized patients, inoculation of Grampositive bacteria especially cocci should be considered as enterococci is one of the most common causative agents of UTIs in inpatients. Thus, media routinely used should support growth of both Gram-negative and Gram-positive bacteria.

On the other hand, anaerobic bacteria are rarely a cause of UTIs, and cultures of anaerobic bacteria are usually indicated only for the patient with increased risk of infection with anaerobic bacteria, and those are usually patients with anatomical abnormalities.

For the diagnosis of Candiduria, blood agar which is used for routine bacterial culture can be used perfectly for its detection and other funguria.

### **2.2 Urinalysis for diagnosis of other infectious diseases**

Many systemic infections other than UTIs can be diagnosed utilizing urine samples. This is applied for viral and bacterial infections. Some of the viruses are directly shed in urine such as human polyomaviruses and congenital cytomegalovirus. Other infections can be detected by markers and antigen secretion in the urine. With the rapid development in diagnostic technologies, urine can be utilized to diagnose even a larger number of infectious agents.

### *2.2.1 Streptococcus pneumoniae*

*Streptococcus pneumoniae* is the number one causative agent of communityacquired pneumonia both in adult and children. In addition, it is underdiagnosed because of the lack of reliable and sensitive diagnostic method. CAP can be diagnosed using various samples including blood, sputum, and urine. Recently, multiple publications [48–50] provided evidence showing that urinalysis and urine specimen can be a very helpful in the diagnosis of CAP with relatively highly sensitive results. Urine immunoassay was used by reference laboratories to determine the course of a complicated outbreak of *S. pneumoniae* complicated by influenza A; this clearly indicates the importance of urine as a diagnostic specimen for the detection of S. *pneumonia* [51].

**191**

infections.

*2.2.6 Dengue virus*

*2.2.7 Zika virus*

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

*Legionella pneumophila* is the most common cause of the life-threatening atypical pneumonia known as legionellosis or Legionnaires' disease. Rapid urinary antigen detection kits are the primary choice for the diagnosis of legionellosis. It is considered to be a reliable diagnostic method for the detection of legionellosis with acceptable sensitivity. New tests and assays such as *Legionella* fluorescence immunoassay have been developed. And they seem promising with papers showing

Tuberculosis is a worldwide health issue. Many factors make tuberculosis hard to control, and one of them is the lack of fast and accurate diagnostic tools. With lipoarabinomannan (cell wall glycolipid of *Mycobacterium tuberculosis*) being secreted in the urine, several assays and tools have been developed to detect this marker of infection. However, no urine test until now is sensitive enough to be adopted for

Infections with polyomaviruses with clinical significance occur generally only in immunocompromised patients; the virus is shed in urine in large quantities. The best way to detect the virus is by electronic microscopy, which is highly sensitive, although it is less sensitive than PCR; however, it might be more reliable clinically. That is because a large portion of the adult population are exposed to the virus, and

Congenital cytomegalovirus is the leading cause of neurological impairment and nongenetic sensorineural hearing loss. The virus can be cultured from urine and diagnosis can be made from various types of specimen which include urine, blood, and saliva [54]. PCR both quantitative and qualitative is widely used for diagnosis of CMV infection. Qualitative PCR test is intended to detect CMV DNA in urine, whereas quantitative PCR test is performed to detect quantitatively CMV DNA in urine specimens as an aid in identifying or management of CMV

Dengue virus is a mosquito-borne disease affecting more than 50 million people worldwide yearly. Urine specimen can be used for the early detection of this virus, although RT-PCR and ELISA along with other new methods all of which utilizing

Zika virus is another mosquito-borne pathogen, and it is endemic to Africa and Southeast Asia. The detection of Zika virus can be achieved by ELISA, but it is usually detected by reverse transcription PCR (RT-PCR) from a serum sample. Some evidence shows that the virus can be detected from mother urine sample even after 10 days of the onset of the disease, which is not feasible with serum samples.

PCR can give positive results to clinically insignificant cases [53].

blood specimen are usually the way to detect dengue virus.

*DOI: http://dx.doi.org/10.5772/intechopen.89231*

a higher sensitivity results [52].

*2.2.2 Legionellosis*

*2.2.3 Tuberculosis*

routine use [17, 18].

*2.2.4 Human polyomaviruses*

*2.2.5 Congenital cytomegalovirus*

*Urine Tests for Diagnosis of Infectious Diseases and Antibiotic-Resistant Pathogens DOI: http://dx.doi.org/10.5772/intechopen.89231*

### *2.2.2 Legionellosis*

*Pathogenic Bacteria*

*2.1.6 Urine culture*

abnormalities.

leukocyte excretion rate. Other microscopic methods may also include counting the leukocyte in the urine. However, as the microscopic method is unpractical for routine use, other easier methods such as leukocyte esterase tests for detection of pyuria can be performed. The leukocyte esterase tests have many disadvantages as it produces false-positive results due the presence of eosinophils in the urine. Decreased positive results or false-negative results of this test are referred to other reasons including elevated level of glucose and protein in the urine or if the patient is treated with certain drugs such as cephalexin or tetracycline [47]. The commercial products are believed to be more efficient, although they have low sensitivity, but they are highly specific, and they provide information about both pyuria and bacteriuria [27].

Urine culture is the gold standard in diagnosing UTI. It is crucial not only for the diagnosis but also to guide appropriate antimicrobial prescription and treatment. Patients with complicated UTIs, those who have suffered from recurrent UTIs, or those who are not responding to the empirical treatment are the ones usually subjected for urine culture. In this regard, the most common used culture media are the blood agar and MacConkey's agar. This is especially true for specimen from outpatients, knowing that almost all UTIs in outpatients are caused by aerobic and facultative Gram-negative bacteria, making it unnecessary to use a medium that is selective for Gram-positive bacteria. However, for the hospitalized patients, inoculation of Grampositive bacteria especially cocci should be considered as enterococci is one of the most common causative agents of UTIs in inpatients. Thus, media routinely used should

On the other hand, anaerobic bacteria are rarely a cause of UTIs, and cultures of anaerobic bacteria are usually indicated only for the patient with increased risk of infection with anaerobic bacteria, and those are usually patients with anatomical

For the diagnosis of Candiduria, blood agar which is used for routine bacterial

Many systemic infections other than UTIs can be diagnosed utilizing urine samples. This is applied for viral and bacterial infections. Some of the viruses are directly shed in urine such as human polyomaviruses and congenital cytomegalovirus. Other infections can be detected by markers and antigen secretion in the urine. With the rapid development in diagnostic technologies, urine can be utilized to

*Streptococcus pneumoniae* is the number one causative agent of communityacquired pneumonia both in adult and children. In addition, it is underdiagnosed because of the lack of reliable and sensitive diagnostic method. CAP can be diagnosed using various samples including blood, sputum, and urine. Recently, multiple publications [48–50] provided evidence showing that urinalysis and urine specimen can be a very helpful in the diagnosis of CAP with relatively highly sensitive results. Urine immunoassay was used by reference laboratories to determine the course of a complicated outbreak of *S. pneumoniae* complicated by influenza A; this clearly indicates the importance of urine as a diagnostic specimen for the detection of S.

support growth of both Gram-negative and Gram-positive bacteria.

culture can be used perfectly for its detection and other funguria.

**2.2 Urinalysis for diagnosis of other infectious diseases**

diagnose even a larger number of infectious agents.

*2.2.1 Streptococcus pneumoniae*

**190**

*pneumonia* [51].

*Legionella pneumophila* is the most common cause of the life-threatening atypical pneumonia known as legionellosis or Legionnaires' disease. Rapid urinary antigen detection kits are the primary choice for the diagnosis of legionellosis. It is considered to be a reliable diagnostic method for the detection of legionellosis with acceptable sensitivity. New tests and assays such as *Legionella* fluorescence immunoassay have been developed. And they seem promising with papers showing a higher sensitivity results [52].

### *2.2.3 Tuberculosis*

Tuberculosis is a worldwide health issue. Many factors make tuberculosis hard to control, and one of them is the lack of fast and accurate diagnostic tools. With lipoarabinomannan (cell wall glycolipid of *Mycobacterium tuberculosis*) being secreted in the urine, several assays and tools have been developed to detect this marker of infection. However, no urine test until now is sensitive enough to be adopted for routine use [17, 18].

#### *2.2.4 Human polyomaviruses*

Infections with polyomaviruses with clinical significance occur generally only in immunocompromised patients; the virus is shed in urine in large quantities. The best way to detect the virus is by electronic microscopy, which is highly sensitive, although it is less sensitive than PCR; however, it might be more reliable clinically. That is because a large portion of the adult population are exposed to the virus, and PCR can give positive results to clinically insignificant cases [53].

#### *2.2.5 Congenital cytomegalovirus*

Congenital cytomegalovirus is the leading cause of neurological impairment and nongenetic sensorineural hearing loss. The virus can be cultured from urine and diagnosis can be made from various types of specimen which include urine, blood, and saliva [54]. PCR both quantitative and qualitative is widely used for diagnosis of CMV infection. Qualitative PCR test is intended to detect CMV DNA in urine, whereas quantitative PCR test is performed to detect quantitatively CMV DNA in urine specimens as an aid in identifying or management of CMV infections.

#### *2.2.6 Dengue virus*

Dengue virus is a mosquito-borne disease affecting more than 50 million people worldwide yearly. Urine specimen can be used for the early detection of this virus, although RT-PCR and ELISA along with other new methods all of which utilizing blood specimen are usually the way to detect dengue virus.

#### *2.2.7 Zika virus*

Zika virus is another mosquito-borne pathogen, and it is endemic to Africa and Southeast Asia. The detection of Zika virus can be achieved by ELISA, but it is usually detected by reverse transcription PCR (RT-PCR) from a serum sample. Some evidence shows that the virus can be detected from mother urine sample even after 10 days of the onset of the disease, which is not feasible with serum samples.

This suggests that detection of Zika virus by real-time RT-PCR from urine specimen can be a valuable diagnostic tool [22].
