Antimicrobial groups based on mechanism of action.
\r\n\t
\r\n\tAdditionally, authors are expected to cover the medicinal effect of tea polyphenols viz. catechins, theaflavins and thearubigins which are the major chemical compounds of tea. Green tea contains a higher quantity of catechins as compared to black tea which becomes transformed into more complex compounds (theaflavins and therubigins) during the manufacturing of black tea. Out of many therapeutic uses these bioactive compounds, protection against cardiovascular diseases, atherosclerosis, cancer, gene mutation, and diabetics have been reported and are more promising. This book will also highlight the nutraceuticals of tea. The catechins along with other various bioactive compounds present in tea have many therapeutic properties which attribute to the development of various food products where tea constitutes as an active ingredient. That is why it is important to stress the potential use of tea and their bioactive constituents (catechins, polysaccharides, vitamins, amino acids etc.) in food products with added nutraceutical values. Finally, the contamination of tea and its effect on our health will also be covered. Tea and its food products may contain various types of contaminations which may include toxic heavy metals, pesticides, microorganisms, and environmental pollutants etc. which are present from tea infusion and from residues. These contaminations which are above the regulatory limit may pose a serious threat to public health. Submitted chapters are expected to contain novel information, be informative as well as thought-provoking.
Increasing resistance to antimicrobial drugs is of major concern worldwide. For many developing countries, the possibility of having cheap antibiotics available may now be threatened. There are antimicrobial resistance issues with most pathogenic bacteria and in virtually all of the opportunistic bacterial-caused infections. This translates into increased healthcare costs. These costs include extended length of hospital stay and increased costs for medical supplies including more expensive antimicrobial drugs. In addition, antimicrobial drug-resistant infections lead to higher rates of mortality, especially in patients who had recent prior exposure to antibiotics [1].
Antimicrobial drugs are classified into groups according to the type of antimicrobial activity. These groups include drugs that inhibit bacterial cell wall synthesis, depolarize the cell membrane, inhibit bacterial protein synthesis, inhibit bacterial nucleic acid synthesis, and inhibit bacterial metabolic pathways. The improper use of these drugs has helped to create resistant bacterial strains. Factors that contribute to resistance include the increased use of all antimicrobial drugs and improper antimicrobial prescribing. Many of the less expensive drugs that have fewer side effects have been used too commonly. Improper prescribing may be choosing broad spectrum or ineffective drugs [2–4].
Many strains of Escherichia coli are not harmful. In fact, these commensal strains in the gut are necessary for the synthesis of vitamin K2, which is an important clotting factor [5]. However, there are pathogenic strains, and these strains may become a larger threat if they possess or acquire certain antimicrobial mechanisms. The main ones of concern are the extended-spectrum β-lactamase (ESBL)-producing strains and the carbapenem-resistant Enterobacteriaceae (CRE) strains. The ESBL strains are resistant to most β-lactam drugs, and the CRE strains are resistant to most carbapenem drugs. Greatly increased healthcare costs are associated with the ESBL and CRE strains. Various studies have shown a hospital stay of up to twice as long and increased costs of 1.5–2.5 times as much [6–8]. One study in the United States estimated the increased costs to be $16,450 per patient [6].
All of the pathogenic strains of E. coli are armed with the same types of potential virulence factors. These factors include a capsule (in some strains), flagella, the lipopolysaccharide (LPS) cell wall, fimbriae, outer membrane proteins (OMPs), a hemolysin, cytolysins, and siderophores. The specific types of some of these virulence factors plus the possession of other toxins and effectors may vary with each individual pathogenic strain [9].
Commensal strains of E. coli are the predominant facultative organism in the human gut. Even though greatly outnumbered by the anaerobic organisms, the E. coli are vital to human health, playing roles in biofilm communities and subsequent digestion of oligosaccharides and polysaccharides, among other things [10, 11]. Unfortunately, there are also several pathogenic strains of E. coli. The classification names of these strains may vary some depending on the source, but for the purposes of this chapter, we will use the following names. There are six strains of potentially pathogenic intestinal-based diarrhea causing E. coli: diffusely adherent E. coli (DAEC), enteroaggregative E. coli (EAEC), enterohemorrhagic E. coli (EHEC), enteroinvasive E. coli (EIEC), enteropathogenic E. coli (EPEC), and enterotoxigenic E. coli (ETEC). In addition, there is one extraintestinal pathogenic strain, uropathogenic E. coli (UPEC), which causes urinary tract infections. There is some evidence that a second extraintestinal strain exists, the meningitis-associated E. coli (MNEC) strain. Findings on MNEC indicate that the infection starts as a blood infection and then gains access to the central nervous system. A majority of MNEC possess the K1 capsular antigen, and there is a high rate of mortality from the meningitis [12]. This chapter will focus on the six intestinal and the UPEC strains.
These strains are sometimes referred to as enteroadherent E. coli (EAEC) (not to be confused with the enteroaggregative strains, which are sometimes referred to as EAggEC). While not known to cause severe diarrheal disease, the DAEC, which are probably a group of related strains, are thought to be responsible for some types of persistent diarrhea in infants. Whether they possess true virulence factors is still under debate, but these bacteria are able to bind to enterocytes (probably via adhesins such as Afa/Dr) and elicit a response in which the microvilli extend and wrap around the bacteria. Diarrhea in association with DAEC has also shown an ability to induce the production of inflammatory cytokines, such as IL-8 [13–15].
The EAEC strains were so named because of their tendency to adhere to enterocytes in dense clusters. The bacteria attach to the microvilli and also to other EAEC bacteria. The EAEC are also a heterogeneous group of strains with a similar pathogenesis, resulting in non-bloody diarrhea. Infection is established by adhering to the microvilli via fimbriae (the aggregative adherence fimbriae—AAF), inducing increased mucus production and biofilm formation, inducing an inflammatory response and production of toxins. The main toxins of the EAEC strains are the EAEC heat-stable enterotoxin (EAST1), which enters the enterocytes and activates guanine cyclase, resulting in increased levels of cGMP in the cell and loss of fluid into the intestinal lumen; the plasmid-encoded toxin (Pet), which disrupts the enterocyte cytoskeleton, resulting in cell detachment; and a Shigella-like enterotoxin (ShET1), a heat-stable toxin which may also result in fluid secretion [16–18].
The most publicized strain of pathogenic E. coli is the EHEC strain. EHEC serotype O157:H7 is well known as the causative agent of outbreaks of food-associated severe diarrhea. Infection with O157:H7 results in sever abdominal cramps and bloody diarrhea and may lead to hemolytic-uremic syndrome (HUS) which can be life-threatening. The most common foods associated with transmission of these bacteria are undercooked meat (especially ground beef), raw milk, and raw vegetables. The EHEC strains do not directly invade the enterocytes, but produce toxins that do enter and severely damage these cells. The responsible cytotoxins are verotoxins I and II (designated as Shiga toxins, Stx-1 and Stx-2). The Shiga toxins are capable of inactivating ribosomes, blocking protein synthesis, and emerging through the basolateral membrane into the subepithelial region. Stx-2 is seen most often in the EHEC strains that cause HUS [19–21].
In infections with EIEC, the bacteria invade by directly entering M cells. The bacteria pass through these cells and then are able to invade the enterocytes via the basolateral membrane, causing severe damage to the intestinal mucosa. The bacteria are also able to spread laterally through the cell side walls to adjacent cells (via actin). This damage results in dysentery (watery diarrhea with pus, mucus, and blood). The EIEC bacteria do not produce toxins, but participate in direct damage and induce production of IL-1 and IL-8. The pathogenic mechanisms and disease symptoms associated with EIEC are so similar to Shigella spp. that differential diagnosis can be difficult. Diagnosis is usually based on physiological and biochemical characteristics that can be detected in the clinical laboratory [19, 22, 23].
The EPEC strains do not directly invade enterocytes. Instead, these bacteria adhere to the microvilli and inject effector proteins into the cell via a type III secretion system (T3SS). One of these effectors is the translocated intimin receptor (Tir), which initiates recruitment of the host cell actin to form a pedestal under the bacteria. The recruitment of actin and formation of the pedestals result in destruction of the rest of the microvilli and also inhibit the transport of Na+ and Cl- in the cell, which results in the subsequent exodus of water into the intestinal lumen. Another effector, the E. coli secreted proteins (Esps), interacts with the host cell cytoskeleton and results in disruption of the cell tight junctions [24–26].
The ETEC strains are a common cause of acute travelers’ diarrhea. These strains usually colonize the proximal small intestine, adhering to the microvilli via various colonization factors including fimbrial, nonfimbrial, helical, and fibrillar types. The EPEC strains secrete two types of toxin: a heat-labile toxin (LT) and heat-stable toxins (STs). The LT is an AB toxin, and the B subunits bind to the monosialoganglioside GM1, which induces the cell to take in the toxin. The LT toxin activates adenylyl cyclase, which increases the cAMP in the cell, resulting in hypersecretion of water and electrolytes into the intestinal lumen. The STs bind to guanylyl cyclase receptors on the microvilli, which stimulate guanylate cyclase and activate the cystic fibrosis transmembrane receptor (CFTR). This results in an increase in cGMP in the cell and impaired absorption of Na+, which causes hypersecretion of water into the intestinal lumen [19, 24, 27].
The UPEC strains are responsible for most uncomplicated urinary tract infections (UTIs). These strains possess a capsule and bind to uroepithelial cells via fimbriae. The interaction of the bacteria with the host cell induces the internalization of the bacteria where the bacteria multiply rapidly and form biofilm-like intercellular bacterial communities (IBCs). The bacteria are shed intermittently from the uroendothelial cells into the lumen of the bladder. UPEC strains produce several types of toxins including hemolysin A (HlyA) which has pore-forming capability and two cytotoxins, cytotoxic necrotizing factor (CNF-1) and secreted auto-transporter toxin (Sat) [19, 28, 29].
As mentioned above, antimicrobial drugs are often classified in groups based on their mechanism of antimicrobial action. Table 1 displays those groups along with examples of the antimicrobial drugs included in each group. The β-lactam drugs, which were among the first antimicrobials to be discovered, target the bacterial cell wall (via peptidoglycan synthesis) and are most useful against gram-positive bacteria (having little effect on gram-negative bacteria because of the lipopolysaccharide cell envelope that protects the thin peptidoglycan cell wall in these bacteria). Over the years, because the β-lactam drugs were readily available and inexpensive and caused few side effects, physicians commonly treated their patients initially with these drugs.
Inhibit cell wall synthesis | β-Lactams Carbapenems Cephalosporins Monobactams Penicillins Glycopeptides |
Depolarize cell membrane | Lipopeptides |
Inhibit protein synthesis | Bind to 30S ribosomal subunit Aminoglycosides Tetracyclines Bind to 50S ribosomal subunit Chloramphenicol Lincosamides Macrolides Oxazolidinones Streptogramins |
Inhibit nucleic acid synthesis | Quinolones Fluoroquinolones |
Inhibit metabolic pathways | Sulfonamides Trimethoprim |
Antimicrobial groups based on mechanism of action.
When bacterial resistance to the β-lactam drugs became an issue (very early on), scientists developed synthetic versions of penicillin such as ampicillin, amoxicillin, and methicillin. In addition, scientists discovered the natural cephalosporin β-lactam drugs. The initial cephalosporins (first generation) were most useful against gram-positive cocci, with some activity against a few gram-negative bacilli. Further development of these drugs has produced second generation (less effective against gram-positive cocci, more effective against gram-negative bacilli); third generation (generally with a broad spectrum of activity against gram-negative organisms); fourth generation (extended-spectrum activity against gram-positive cocci and gram-negative bacilli); and recently, fifth generation (hopefully effective against various multidrug-resistant organisms), with more still in development. Other β-lactam drugs developed during this time frame were the carbapenems (broad-spectrum activity) and monopenems (aztreonam—activity against gram-negative aerobic bacteria) [30–32].
Differences in structure, metabolism, virulence factors, etc., between gram-negative and gram-positive bacteria predict which antimicrobial drug groups may be effective. Fewer of the drug groups have good activity against gram-negative bacteria. Those groups include some of the β-lactam drugs (especially second-, third-, and fourth-generation cephalosporins): aminoglycosides, fluoroquinolones, trimethoprim/sulfamethoxazole (TMP/SXT), and nitrofurans (for UTIs) [33]. Intestinal infections with E. coli are most commonly self-limiting and require supportive therapy (antiemetics, antidiarrhetics, rehydration) only. Severe or recurring infections (e.g., traveler’s diarrhea) may be treated with fluoroquinolone drugs. Acute dysentery caused by EIEC strains may be treated with fluoroquinolones or appropriate cephalosporins. For infections caused by EHEC, antimicrobial therapy is contraindicated as it greatly increases the risk for development of HUS. UTIs caused by UPEC strains are usually treated with antimicrobial drugs and uncomplicated UTIs with nitrofurantoin or TMP/SXT; complicated UTIs may also be treated with fluoroquinolones [34–37]. Infections with ESBL or CRE strains severely limit treatment options. For ESBL strains, carbapenems may still be an option or newer β-lactam/β-lactamase inhibitor drug combinations; for CRE strains, gentamicin, amikacin, colistin, tigecycline, and fosfomycin may be options. Unfortunately, some ESBL and CRE strains may be resistant to even some of these drugs [38–40].
At the beginning of antimicrobial drug resistance, physicians did not realize how the various drugs affected the bacteria. In addition, in an effort to begin antimicrobial therapy as quickly as possible, physicians often ordered a broad-spectrum drug before knowing the causative agent of the infection. These issues (among others) have led to a large amount of resistance to β-lactam drugs, especially among the gram-negative bacteria. Bacteria that produced β-lactamases (enzymes that inactivate β-lactam drugs) were identified as early as the 1940s (around the same time as penicillin was discovered), and the number of different β-lactamases produced has increased over the years to around 1000 [2–4, 41].
The issue of resistance is not just with the β-lactam drugs. Over the 70 plus years that antimicrobial drugs have been in existence, resistance mechanisms have been seen for most of these drugs. It does not seem to take the bacteria very long from initial use of a drug to development of resistance to that drug. Important resistant milestones include resistance to aminoglycosides and tetracycline in the 1960s, vancomycin in the 1980s, fluoroquinolones in the 1990s, and linezolid in the 2000s [42]. In addition, some of the bacteria have become resistant to multiple antimicrobial agents from many of the drug classes. These multidrug-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), are currently a major cause of morbidity and mortality [43].
Similar to the threat of MRSA, members of the gram-negative Enterobacteriaceae, in particular E. coli and Klebsiella pneumoniae, include strains that are ESBLs and CREs. These organisms can be resistant to most commonly used antimicrobials, which makes the infections they cause extremely difficult to treat, leading to increased morbidity and mortality (and healthcare costs) [44, 45].
There are four general antimicrobial resistance mechanisms that bacteria use. These are limiting uptake of the drug, modifying the target of the drug, inactivating the drug, and active efflux of the drug. These mechanisms may be located on the bacterial chromosome and occur naturally in all members of a species (intrinsic) or come from other bacteria, usually via a plasmid (acquired). Intrinsic resistance genes may be expressed constitutively (usually at a low level) or be induced by the presence of antimicrobial drugs. Gram-negative bacteria widely use all four of these mechanisms and are very capable of horizontal transfer of resistance elements. Table 2 shows which resistance mechanisms and genes are associated with resistance to various antimicrobial drugs [43, 46, 47].
Antimicrobial agents | Mechanisms of resistance | Genetic basis |
---|---|---|
β-lactams Penicillins Cephalosporins Monobactams Carbapenems | β-lactamases—inactivate drugs Active efflux | ampC bla genes—plasmid (TEM, SHV, CTX-M, NDM) acrAB(tolC), acrAD(tolC) |
Aminoglycosides Amikacin Gentamicin Tobramycin | Aminoglycoside modifying enzymes Modify target—16S rRNA Active efflux | aac, ant, aph—plasmid amrA, rmtB mdtEF(tolC) |
Tetracyclines Tetracycline | Limiting uptake Active efflux | ompF acrAB(tolC) tetA, tetB—plasmid |
Chloramphenicol | Limiting uptake Active efflux | ompF acrAB(tolC) |
Fluoroquinolones Ciprofloxacin Norfloxacin | Limiting uptake Modified target—gyrase Modified target—topoisomerase IV Active efflux | ompF gyrA parC acrAB(tolC), acrEF(tolC), mdtABC(tolC) |
Metabolic pathway inhibitors Trimethoprim/Sulfamethoxazole | Target enzyme modification | TMP—dhfr SXT—dhps |
Common antimicrobial resistance genes and mechanisms in Escherichia coli.
Gram-negative bacteria have an advantage in combating drugs because of the structure and functions of the LPS cell wall, which provides a natural barrier to certain molecules. The LPS is generally hydrophobic which limits access to small hydrophilic drugs, such as the β-lactams. These hydrophilic drugs gain access by traveling through the OMPs. The main OMPs in E. coli are OmpF and OmpC. In addition to the β-lactams, other drugs that may use the porin channels are chloramphenicol, fluoroquinolones, and tetracycline. Hydrophobic drugs such as the aminoglycosides and the macrolides gain access by permeating through the LPS layer. There are two main mechanisms that are used to limit access to drugs via porins: a decrease in the number of porins or a change in charge, within the porin channel, which reduces its function or binding properties. In E. coli porin production may be reduced dramatically or even stopped, or a different porin may be produced instead [48, 49].
Gram-negative bacteria make use of the modifying of drug targets against several of the antimicrobial groups including β-lactams, aminoglycosides, fluoroquinolones, and the combination drug TMP/SXT. Even though not as widely used as in gram-positive bacteria, the gram-negative bacteria are able to produce penicillin-binding proteins (PBPs) that are resistant to some β-lactam drugs. PBPs are actually peptidases that are involved in the making of the peptidoglycan cell wall. Penicillin drugs that are able to bind to PBPs inhibit the assembly process. There are several different native PBPs produced by E. coli, some of which have reduced binding affinity for some of the β-lactam drugs. No acquired modified form of PBP has been shown to be significant in β-lactam resistance in E. coli [50, 51].
The aminoglycoside drugs inhibit protein synthesis by binding to the bacterial 30S ribosomal subunit at the A-site of the 16S rRNA. Bacteria are able to modify the ribosomal subunit via acquisition of plasmids carrying 16S rRNA methyltransferases. The methyltransferases are able to modify the structure of the 16S rRNA, which decreases the ability of the drug to bind to it. Several of these methyltransferases have been identified and characterized. The genes involved include armA (for aminoglycoside resistance methylase) and several rmt (for ribosomal methyltransferase) genes, with rmtB being the most common. The bacteria quite often possess several of these genes simultaneously. These genes most often confer clinically significant resistance to amikacin, gentamicin, and tobramycin, among other aminoglycosides [52–56].
The fluoroquinolone drugs interfere with nucleic acid synthesis during DNA replication by inhibiting either DNA gyrase or topoisomerase IV. Resistance to these drugs occurs commonly from mutations in either the chromosomally encoded GyrA subunit of gyrase (gyrA gene) or the ParC subunit of topoisomerase IV (parC gene). These mutations decrease the binding ability of the drugs, most commonly ciprofloxacin and norfloxacin. There is also some evidence that low-level resistance may be acquired via plasmids carrying quinolone resistance (qnr) genes [56–58].
The combination drug TMP/SXT is currently a common choice for treatment of UTIs. Both of these drugs target enzymes in the bacterial folate biosynthesis pathway via competitive inhibition. Trimethoprim is an analog of the natural substrate of the dihydrofolate reductase (DHFR) enzyme, and SXT is an analog of p-amino-benzoic acid, the natural substrate of the dihydropteroate synthase (DHPS) enzyme. This competitive binding blocks the binding of the natural substrate and stops the pathway at that point. Since TMP and SXT affect two different enzymes on the same pathway, the combination drug makes an effective treatment. Chromosomal mutations (often single point mutations) in the dhfr or dhps genes are commonly the cause of resistance to these drugs [59, 60].
Drug inactivation is accomplished in one of two ways: by actual degradation of the drug or by transfer of a chemical group to the drug. Gram-negative bacteria use drug inactivation against β-lactams and aminoglycosides. The β-lactam drugs are universally inactivated by β-lactamase enzymes, which degrade the drugs, and E. coli produces several of these. The aminoglycoside drugs are inactivated fairly universally by enzymes that transfer one of three small chemical groups to the drug. These enzymes include the acetyltransferases (AACs, aac genes), nucleotidyltransferases (ANTs, ant genes), and the phosphotransferases (APHs, aph genes) [43, 49, 61].
The β-lactam drugs all share a specific core structure, which consists of a four-sided β-lactam ring. The β-lactamases (also originally called penicillinases and cephalosporinases) are capable of inactivating β-lactam drugs via hydrolyzation of a specific site in the β-lactam ring structure causing the ring to open. The drugs are then not able to bind to their target proteins, the PBPs. Within the large number of β-lactamases which have been identified, there are enzymes which can inactivate any of the current β-lactam drugs. The production of β-lactamases is the most common resistance mechanism used by gram-negative bacteria against β-lactam drugs [46, 62].
The β-lactamase enzymes can be classified based on their primary structure or functional characteristics. Structurally they are placed into four main categories (A, B, C, or D). There are three functional groupings: the cephalosporinases, the serine β-lactamases, and the metallo-β-lactamases. These enzymes are also commonly referred to by their enzyme family, for example, the TEM (named after the first patient) family, the sulphydryl variable (SHV) family, and the CTX (preferentially hydrolyze cefotaxime) family [56, 63].
The first β-lactamase to be characterized was from E. coli and is chromosomally encoded by the ampC gene (so named for ampicillin resistance). This gene is constitutively expressed at a low level, but mutations may result in overexpression of the gene. The AmpC β-lactamases are most effective against the penicillins and some first-generation cephalosporins. There are also many plasmid-borne β-lactamases, which carry a variety of bla genes (β-lactamase genes). Because these β-lactamases confer resistance to later generation cephalosporins, they were designated as ESBLs and include the TEM, SHV, and CTX-M enzyme families. The most commonly seen of these in E. coli are the CTX-Ms. The ESBLs may also be resistant to multiple drug classes but are generally sensitive to β-lactamase inhibitors. The β-lactamase inhibitors are structurally similar to β-lactamases and have weak antimicrobial ability alone but work synergistically in combination with a β-lactam drug [56, 64–67].
Recently, there has been emergence of β-lactamases that are active against the carbapenems (carbapenemases), found primarily in the Enterobacteriaceae. Bacterial strains that carry these are known as CRE strains. The carbapenemases are all metallo-β-lactamases (MBLs), and the most widely distributed are the IMP-1 (for imipenem resistance) and VIM-1 (Verona integron-encoded MBL) types. A new MBL has recently been identified, mainly in strains of E. coli. It has been designated as New Delhi MBL (NDM-1). The CRE strains are usually resistance to all the β-lactam drugs and are not inactivated by the standard β-lactam/β-lactamase inhibitor combination drugs. There is a newer β-lactamase inhibitor, avibactam, which has been approved for use with ceftazidime against gram-negative bacteria. In addition, avibactam is being tested for use with aztreonam against CREs [62, 66–68].
Bacteria possess methods for disposal of toxic substances to the outside of the cell. The most commonly used mechanism is the efflux pump. Most bacteria have chromosomally encoded efflux pump genes. Some of these pumps are expressed constitutively, and expression of others is induced by various environmental stimuli. Many of these pumps are capable of transporting a variety of substances and are also described as multidrug (MDR) efflux pumps. There are five efflux pump family groups: the ATP-binding cassette (ABC) family, the multidrug and toxic compound extrusion (MATE) family, the major facilitator superfamily (MFS), the small multidrug resistance (SMR) family, and the resistance-nodulation-cell division (RND) family. The RND pumps are generally found only in gram-negative bacteria as these pumps are multicomponent pumps that function in association with an OMP [69–72].
There is only one ABC efflux pump in E. coli that is known to contribute to antimicrobial resistance. That is the MacAB transporter that confers resistance to some macrolides [73]. There is also only one MATE efflux pump found in E. coli, the NorE pump which is able to transport fluoroquinolones. It is still in question if the NorE pump has a clinically significant impact on antimicrobial resistance [74, 75]. There are five known MFS efflux pumps found in E. coli. These are capable of transporting macrolides (MefB and MdfA pumps), fluoroquinolones (QepA2, EmrAB-TolC, and MdfA pumps), tetracycline (EmrAB-TolC and MdfA pumps), trimethoprim (Fsr pump), and chloramphenicol (MdfA pump). In addition, there are several MFS pumps that may be acquired by E. coli (e.g., via plasmids) that are specific for tetracyclines, with tetA and tetB being the most common [76, 77]. There are no clinically significant SMR efflux pumps found in E. coli [78].
The RND efflux pumps are the most clinically significant pumps found in gram-negative bacteria. These pumps consist of three components (tripartite): an inner membrane transporter, an outer membrane porin, and a periplasmic accessory protein that functions to connect the other two components. In E. coli, the OMP that is associated with all of the antimicrobial efflux pumps is TolC. There are five known RND pumps in E. coli: AcrAB-TolC, AcrAD-TolC, AcrEF-TolC, MdtABC-TolC, and MdtEF-TolC. AcrAD-TolC has been shown to efflux aminoglycosides and β-lactams. AcrEF-TolC has been shown to efflux quinolones and tigecycline. MdtABE-TolC has been shown to efflux quinolones. MdtEF-TolC has been shown to efflux erythromycin. The level of expression of these four pumps is relatively low, and if operating alone, the amount of antimicrobials effluxed would probably not be significant. Because E. coli has five efflux systems plus multiple other types of antimicrobial resistance mechanisms in play, these pumps undoubtedly help out. The other RND efflux pump in E. coli, AcrAB-TolC, is the most clinically significant and accounts for major antimicrobial efflux. This pump has been shown to efflux β-lactams, fluoroquinolones, tetracyclines, chloramphenicol, and lincosamides [72, 79, 80].
For many strains of pathogenic E. coli, the most common course of therapy is supportive and does not require the use of antimicrobial drugs, or in the case of EHEC, antimicrobial therapy is not recommended. For severe intestinal infections and UTIs, antimicrobial therapy may be necessary. Unfortunately with the issue of ever increasing antimicrobial resistance, the antimicrobial options are becoming fewer. With the emergence of ESBL and CRE E. coli strains, the options have gotten extremely limited, and antimicrobial development has not been able to keep up with the demand. Hopefully the newer carbapenem/β-lactamase inhibitor combination drugs and other drugs being developed under the tetracycline and aminoglycoside drug classes will prove to be equal to the task or at least keep the bacteria under control until better options become available.
Azad Jammu and Kashmir valley extends between 34°22′25 North latitude and 73°28′14 East longitude. Muzaffarabad is capital city of Kashmir and total area covered by Kashmir valley is 13,297 square kilometers. Estimated population of Azad Jammu and Kashmir is about 4-million. Mean maximum temperature was documented during summer (16 °C–24 °C) while −4 °C was recorded mean minimum temperature during winter. AJK is rich in diversity of plants because of its expanded habitations, such as streams, springs, nullahs, lakes, rivers, steep mountain slopes and roads, waste lands and cultivated fields, etc.
\nThe area of valley can be divided into two geographical zones; East and North are mostly hilly and mountainous categorized by undulating terrain, deep ravines, and rugged (Neelum, Muzaffarabad, Hattian, Bagh, Haveli, Poonch, and Sudhnoti) while South and West are valleys and plains (Kotli, Mirpur, Bhimber) (Figure 1).
\n(a) Sudhen Gali district Bagh (b) Tolipeer district Poonch (c) Neelum valley (d) Areng khel Neelum valley (e) Leepa valley (f) Las Dana.
In AJK, vegetation can be divided into four groups:
Subtropical vegetation is further divided into Dry scrub forest vegetation and Pine forest vegetation
Temperate forest vegetation further divided into Moist Temperate and Dry Temperate Forest vegetation
Sub alpine vegetation
Alpine vegetation
The Himalaya Kashmir is documented as worldwide epicenter of endemism and plant diversity. Accordance to the report of Pei [1], in Himalayan range, total number of plant species is about 25,000 and total number of angiosperms in Kashmir Himalaya is about 3,054 [2]. About 80% endemic angiosperms is in Pakistan are confined to Northern and Western mountains [3, 4]. 70–80% of population in this region depends on traditional medicines for health care and in Himalayan ranges; at least 70% of the medicinal plants and animals in the region consists of wild species [5]. A total of 104 medicinal plant species including tree, shrubs and herb species used ethnobotanically by the local people of Muzaffarabad were reported from Machyara National Park Muzaffarabad [6, 7]. Most of People living in mountains regions use plants in different ways such as medicines, fire wood, timber wood, food, fodder etc. [8].
\nMedicinal plants are considered as safe medication and it is also naturally valuable remedy for many human sufferings in rural and remote hilly regions of Kashmir [9]. Due to the lack of advanced medicinal services, usage of flora as ethno medicine is renowned. Traditional curative usage of herbal plants by indigenous populations of AJK has been stated ([10] a&b; [11]). Saghir et al. [12] found 53 plant species useful mostly as medicinal, fuel, fodder, fruit, timber and vegetables reported from Chikar and allied areas of District Muzaffarabad. Gorsi and Shahzad [13] documented medicinal flora and suggested regeneration work to save the traditional knowledge about plants of Dirkot. Ishtiaq et al. [14] stated that plants are indirectly related to the culture and they stated 36 plant species used for the treatment of various diseases in Samahni valley. Khan et al. [15] indicated that the inhabitants of Poonch Valley utilized 169 plant species for more than 30 domestic needs. Ajaib et al. [16] provided ethnobotanical data on medicinal flora of district Kotli by reporting 38 species of shrubs. Saqib et al. [17] studied the medicinal flora of mountainous areas of AJK. Some of medicinally important plant species include Saussurea lappa, Aconitum heterophyllum, Jurinea dolomea, Bistorta amplexicaule, Plectranthus rugosus,, Geranium wallichianum, Ajuga bracteosa, Taraxacum offincinale, Quercus incana, Berberis lyceum and Viola canescens [18]. 70% of the therapeutic flora in the area comprise of wild species; 70–80% inhabitants dependent on traditional medications [19]. People of Azad Jammu & Kashmir are still dependent mainly on medicinal plants for folk remedies, hence creating immense pressure on native vegetation by overexploiting them, particularly in the mountainous region of Kashmir [20].
\nThe original printed data of plants as medication initiating from the Himalayas date back to ancient scripts of the Rigveda, monitored by Auryveda (600–100 BC)and Atharveveda (2000–1000 BC). Northern mountains of Pakistan located at intersection of three Mountain ranges i.e., Himalaya, Karakorum and Hindu Kush are well recognized for their biodiversity [21]. Azad Jammu and Kashmir is endowed with productive variety of medicinal plants. It has been stated on many curative practices of plants by the indigenous populations [10, 14, 22, 23]. For above 10,000 classes of curative and scented plants, 600 million folks exist in in Himalayan section. In Himalayan ranges, 70% of therapeutic flora comprise of wild species [19]. Northern regions including Kashmir are in pressure from indigenous people and tourists. Primary reasons include unselective displacing and storing systems of remedial plants. Therefore, therapeutic tradition needs to be recognized and protected. Hundreds of species are currently endangered for the reason of excessive harvesting. Northern mountainous areas have several climatic and vegetation regions. These diverse natural regions have distinctive ethnobotanical vital plants that are significant for the economy of a nation. For traditional medications People of AJK are generating massive stress on flora by damaging those [20]. In north-western zones of Pakistan, several ethnobotanical trainings have been convoyed and which have assembled evidence on the usage of therapeutic flora [4]. The valuable ethnobotanical data is declining owing to the deficiency of awareness and information.
\nAzad Jammu and Kashmir is gifted with dynamic variety of medicinal plants. Below, we discuss some wild fruits and vegetables commonly used by indigenous people of AJK. Main wild fruits of the valley are Ficus palmata Malus pumila, Prunus persica, Prunus cerasus, Morus alba, Diospyros lotus, Rubus fruticosus, Vitis vinifera, Viburnum foetens and Punica granatum. Fruit of Juglans regia L. (Juglandaceae) is used as dry fruit. Fruit also remove gall bladder stones and is aphrodisiac. Fruits of Morus nigra L. (Moraceae) are dried and sold in market as a dry fruit. Fresh fruit is ground and used as tonic and for cough and throat irritation. Fruits of Rubus ellipticus Smith (Rosaceae) are edible. Withinia somnifera (L.) Dunal (Solanaceae) is used in Ayurvedic medicinal purposes and fruits are edible. Fruits of Zanthoxylum alatum DC. (Rutaceae) are aromatic, condiment and carminative and are used in sauce. They are also used for the treatment of piles. Ziziphus nummularia (Burm.f.) Wight & Arn. (Rhamnaceae) fruit is edible and laxative and leaves are used as fodder for goat. Punica granatum L. (Punicaceae) is used as treatment for Cancer, Osteoarthritis and other diseases. It has been used in natural and holistic medicine to treat sore throats, coughs, urinary infections, digestive disorders, skin disorders, arthritis. Pyrus pashia L. (Rosaceae) fruit is superlative to eat when it is slightly decaying. It is set apart from the cultivated pears by having a grittier quality. The fully ripe fruit has a reasonable taste and, when bletted, is sweet and very pleasant to eat. Viburnum grandiflorum Wall. (Caprifoliaceae) fruit is edible used against malaria [24] (Table 1). Miscellaneous uses of plants in the area comprise spices and condiments, ornamental plant species, vegetables and pot herbs, s agricultural tools, basket making, cosmetics, dish cleaner, house decoration, feed, field fencing, furniture, narcotics, packing material, curing snake and scorpion bite, soil binder, sticks and handles, shade tree, herbal tea and for making utensils. Maswak made from the roots of J. regia and branches of A. modesta, O. ferruginea and Z. alatum is used for cleaning their teeth. Plants are used as a major source of veterinary medicine. Interest of such use in the veterinary sector has resulted primarily from the increasing cost of livestock maintenance and the introduction of new technology in the veterinary medicines and vaccines. The important medicinal plant species showed the highest fidelity such as: Rumex nepalensis, Primula denticulata, (100%) used for dysuria, red urination, Skimmia laureola (100%), Swertia paniculata (99%), and Angelica glauca (97%), used for ague, cold, shivering, gastric ailments, Melia azedarach (100%), used to reduce intestinal worm load in cattle showing the conformity of knowledge on these species (Table 2). Plant communities have been largely disturbed due to deforestation for fuel, over consumption of medicinal resources for the population explosion, treatment of diseases, increased tourism and lack of awareness. Vulnerable species include Sorghum halepense, Acacia modesta and Solanum nigrum. Medicinal species like Cissus carnosa, Butea monosperma Ajugabracteosa, Mallottus philippinensisand Zanthoxylum armatum are critically endangered. Among endangered species, Juglans regia, Olean ferruginaea, Phyllanthus emblica, Viola canescens are the notable species. Some medicinal plants like G. wallichianum, J. dolomiaea, A. bracteosa, B. amplexicaule, S. lappa, A. heterophyllum, and B. lyceum are on the edge of extinction due to high rate of intake [25].
\n\n | Botanical name | \nFamily | \nCommon name | \nTraditional uses | \n
---|---|---|---|---|
1. | \n\nAjuga bracteosa\n Wall.ex. Benth. | \nLamiaceae | \nHeri-booti | \nA decoction is used for curing intestinal ulcer, jaundice, throat infection and high blood pressure | \n
2. | \n\nArgemone mexicana L. | \nPapaveraceae | \nDudhli kandyari | \nSeeds are analgesic and laxative. | \n
3. | \n\nAlstonia scholaris (L.) R.Br. | \nApocynaceae | \n— | \nThe bark is used to treat malaria, fever, asthma and tumors. | \n
4. | \n\nAmaranthus viridis L. | \nAmaranthaceae | \nGanar | \nLeaves are used on scorpion sting and snake bite. Root juice is used to treat constipation and inflammation during urination | \n
5. | \n\nAlternanthera pungens Kunth | \nAmaranthaceae | \nItsit | \nRoots and leaves are blood purifier and diuretic. | \n
6. | \n\nAnisomeles indica (L.) S. Kurz. | \nLamiaceae | \n— | \nDecoction of leaves is anti-rheumatic and used in stomachic and toothache. | \n
7. | \n\nAchyranthes aspera L. | \nAmaranthaceae | \nPuth kanda | \nLeaves are used in pneumonia and asthma. | \n
8. | \n\nAlbizzia lebbeck (L.) Benth. | \nMimosaceae | \nSreeia | \nSeeds are used for curing kidney infection | \n
9. | \n\nBauhinia veriegata L. | \nCaesalpiniaceae | \nKatchnar | \nFruit is edible and useful for leprosy and skin diseases. | \n
10. | \n\nButea monosperma\n (Lam.) Taubert | \nPapilionaceae | \nChechra | \nGum is tonic given for backache after birth. | \n
11. | \n\nBuddleja asiatica Lour. | \nBuddlejaceae | \nBatta | \nUsed for skin disease, and as a cure for loss of weight | \n
12. | \n\nBarleria cristata L. | \nAcanthaceae | \n— | \nSeeds are antidote for snake bites and for serious catarrhal infections | \n
13. | \n\nBoerhavia diffusa L. | \nAmaranthaceae | \nSanati | \nImprove eyesight, diuretic and useful in controlling blood sugar levels | \n
14. | \n\nBuglossoides arvensis (L.) Johnston | \nBoraginaceae | \nKalu | \nLeaves infusion is sedative | \n
15. | \n\nCroton bonplandianus\n Baill | \nEuphorbiaceae | \n— | \nLeaves control blood pressure | \n
16. | \n\nCissampelos pareira L. | \nMenispermaceae | \nBatrarr | \nA rhizome decoction and pounded leaves are externally applied as a febrifuge and stomachic, cough and snake bite | \n
17. | \n\nCarissa opaca Staplf ex. Haines | \nApocynaceae | \nGrunda | \nFruit is edible and blood purifier | \n
18. | \n\nCassia fistula L. | \nCaesalpiniaceae | \nAmaltas | \nThe root helps in reliving the symptoms of fever, asthma, leprosy and heart related diseases | \n
19. | \n\nChenopodium album L. | \nChenopodiaceae | \nBathwa | \nThis plant is laxative | \n
20. | \n\nCissus carnosa (L.) Lamk | \nVitaceae | \nDakh | \nFruit is good for abdominal diseases | \n
21. | \n\nCalotropis procera\n | \nAsclepiadaceae | \nDesi akk | \nPlant extract is applied on dog bite. Latex is used for skin diseases and ring worm. | \n
22. | \n\nCannabis sativa L. (Ait.) | \nCannabinaceae | \nBhang | \nRoot is used for liver disorders. Leaves and flowers are analgesic, sedative, narcotic, laxative and aphrodisiac. | \n
23. | \n\nCascuta reflexa Roxb | \nCuscutaceae | \nNeel Dhari | \nIts infusion is anti-lice. It is also used in skin diseases and weaknesses of children. | \n
24. | \n\nChenopodium album L. | \nChenopodiaceae | \nBathwa | \nLeaves are anthelmintic and laxative | \n
25. | \n\nConvolvulus arvensis L. | \nConvolvulaceae | \nRawari | \nRoot is diuretic and purgative | \n
26. | \n\nDiplocyclos palmatus\n (L.) C. Jeffery | \nCucurbitaceae | \n\n | Plant is used for skin diseases and cough | \n
27. | \n\nDodonea viscosa (L.) Jacq. | \nSapindaceae | \nSanatha | \nDecoction of wood is used as febrifuge and skin diseases | \n
28. | \n\nDalbergia sissoo Roxb. | \nPapilionaceae | \nTali | \nBranches kill worms in sthe teeth | \n
29. | \n\nEugenia jambolana Lam. | \nMyrtaceae | \nJaman | \nIt is used for the treatment of cancer | \n
30. | \n\nFumaria indica\n (Hausskn.)Pugsley | \nFumariaceae | \nPapra | \nIts infusion is used as diaphoretic, blood purifier and antipyretic | \n
31. | \n\nFicus palmate Forssk | \nMoraceae | \nPhugwara | \nFruit is laxative, soothes bee sting | \n
32. | \n\nGymnosporia royleana (Wall.ex Lawson) Cuf | \nCelastraceae | \n\n | It is used for treatment of cough, asthma, tonic and abdominal pain | \n
33. | \n\nGalium aparine L. | \nRubiaceae | \nLahndara | \nPlant extract is diuretic | \n
34. | \n\nHedera nepalensis\n K.Koch. | \nAraliaceae | \n\n | Leaves are used for treatment of diabetes | \n
35. | \n\nJusticia adhatoda L. | \nAcanthaceae | \nBhakar | \nIt is used to treat colds, coughs, asthma, fevers, skin infections and inflammations | \n
36. | \n\nJuglans regia L. | \nJuglandaceae | \nKhor | \nRoot and leaves are antiseptic. Fruit is aphrodisiac, remove stones in gall bladder | \n
37. | \n\nMalva parviflora L. | \nMalvaceae | \nSonchul | \nLeaves extract is anthelmintic | \n
38. | \n\nMallotus philippinensis (Lam.) Muell. | \nEuphorbiaceae | \nKamella | \nFruit is purgative and anthelmintic | \n
39. | \n\nMedicago polymorpha L. | \nPapilionaceae | \nSriri | \nLeaves are helpful in digestive disorders | \n
40. | \n\nMelia azadarach (L.) | \nMeliaceae | \nDraik | \nLeaves and fruit are blood purifier, antipyretic and antidiabetic | \n
41. | \n\nMalvastrum\n \nCoromandelianum (L.) Garcke | \nMalvaceae | \n\n | Leaves paste relieve pain. Flowers are diaphoretic | \n
42. | \n\nMorus nigra L. | \nMoraceae | \nKala Toot | \nFruit is tonic and used for throat irritation and cough | \n
43. | \n\nMentha longifolia Benth | \nLamiaceae | \nJangli podina | \nLeaves are carminative and stimulant. Leaves are antispasmodic | \n
44. | \n\nNasturtium officinale R.Br. | \nBrassicaceae | \nChooch | \nThe leaves and stem are used for internal tumors, scurvy and anemia | \n
45. | \n\nNerium indicum L. | \nApocynaceae | \nGandeera | \nLeaves decoction is applied on skin diseases | \n
46. | \n\nOxalis corniculata L. | \nOxalidaceae | \nKhati Buti | \nLeaves decoction is used in dysentery and fever | \n
47. | \n\nPlantago lanceolata L. | \nPlantaginaceae | \n\n | Leaf extract is applied to wounds, sores and bruises; seeds are purgative | \n
48. | \n\nPinus roxburghii\n Sargent | \nPinaceae | \nCheer | \nResin is used for bleeding wounds and tumors and cough. Leaves and bark powder is useful for dysentery | \n
49. | \n\nPapaver dubium L. | \nPapaveraceae | \nJangli post | \nIts infusion is blood purifier, antipyretic, and diaphoretic | \n
50. | \n\nPeriploca aphylla\n Decne | \nAsclepidiaceae | \nBata | \nIt is used for treatment of swellings and tumors | \n
51. | \n\nRumex dentatus L. | \nPolygonaceae | \nHerfli | \nLeaves are astringent and diuretic | \n
52. | \n\nRhamnus triquetra\n (Wall.) Brandis | \nRhamnaceae | \nClader | \nFruit and leaves are used in hemorrhagic septicemia | \n
53. | \n\nRanunculus muricatus L. | \nRanunculaceae | \nKor- Kandoli | \nFruits and leaves are useful on bursts and tumor | \n
Important medicinal plant species with traditional uses in Azad Jammu and Kashmir.
\n | Scientific name | \nFamily | \nCommon name | \nEthno veterinary practices | \nAilments | \n
---|---|---|---|---|---|
1. | \n\nAmaranthus viridis L. | \nAmaranthaceae | \nSafed kannar | \nDecoctions | \nMalaria | \n
2. | \n\nArisaema flavum\n (Forssk.) Schoot | \nAraceae | \nToosh | \nInfusion | \nMouth and foot disease of cattle | \n
3. | \n\nArisaema jacquemontii Blume | \nAraceae | \nTooshganda | \nAs whole plant | \nInflammation, cholera, dysentery, flu, dyspepsia and snake bite | \n
4. | \n\nSenecio chrysanthemoides DC. | \nAsteraceae | \nBghoo | \nDecoction | \nAntiscorbutic, anthelmintic, and diaphoretic | \n
5. | \n\nLactuca brunoniana (DC.) Wall. ex C.B. Clarke | \nAsteraceae | \nKorijari | \nThe whole plant | \nPinworms | \n
6. | \n\nAesculus indica (Wall. ex Cambess.) Hook. | \nSapindaceae | \nBankhorr | \nDecoction/dried plant powder is mixed with gurr and flour | \nIndigestion and constipation | \n
7. | \n\nMelia azedarach L. | \nMeliaceae | \nDrek | \nPowder | \nAnthelmintic | \n
8. | \n\nFicus palmata Forssk. | \nMoraceae | \nPagaaar | \nWhole | \nAnorexia | \n
9. | \n\nBergenia ciliata (Haw.) Sternb. | \nSaxifragaceae | \nButpeewa | \nPowder | \nStomachic and intestinal troubles | \n
10. | \n\nFagopyrum acutatum (Lehm.) Mansf. ex K. | \nPolygonaceae | \nKhattra | \nAs fodder | \nAntimicrobial, bactericidal and diuretic | \n
11. | \n\nPrimula denticulata Sm. | \nPrimulaceae | \nChiatpatra | \nDecoction | \nDysuria, hepatic fever and hemoglobinuria | \n
12. | \n\nSorbaria sorbifolia (L.) A. Braun | \nRosaceae | \nKarleee | \nAs fodder | \nStimulant | \n
Ethno-veterinary practices of important plants in Azad Jammu and Kashmir.
Morel collection is an important activity during spring season and villagers take keen interest in collection of morels as it provides them a source of income. Mushroom flora and species diversity as important component of the natural environment in Azad Jammu and Kashmir. Wild mushrooms are sources of edible proteins, dietary fiber, essential amino acids, carbohydrates, and are an important source of food, livelihood, and traditional ethnobotanical health care. Kashmir region is rich with unknown macro fungal wealth. Among total morel population of Pakistan, 90% was reported from the Himalayan mountain ranges of Northern Pakistan. Wild edible fungi dominate the global morel trade, with an estimated value of more than US$2 billion. Ullah et al. [26] reported 56 wild edible mushrooms in Pakistan, of which 44 are from the Kashmir region. Important species include Agaricus campestris, Hydnum imbricatum, Sparassis crispa, Morchella esculenta, M. crassipes, M. elata, M. conica, Pleurotus ostreatus, Lycoperdon gemmatum, Helvella crispa, Tricholoma megnivelare and Gyrometra esculenta. The local communities of valley well recognize the habitats, morphological features, and qualities of these mushrooms. Ethno mycological data were collected through the use of a questionnaire and found that these species have great medicinal value against different ailments. Four species (A. campestris, H. imbricatum, P. ostreatus, and S. crispa) are highly recommended for their frequent use as food based on nutritional analysis (proteins, fats, fiber, and moisture). The major identified species from AJK are Agaricus arvensi, Amanita vaginata, A. fulva, Cantharellus cinereus, Coprinus micaceus, C. comatus, C. domesticus, Cycoperdon perlatum, Daedalea quercina, Helvella crispa, Hygrophuorus melizeus, Lepista nuda, Lactarius turpis, Marasmius alliaceus, Panaeolus campanulatus, Pleurotus ostreatus, Trametes versicolor, and Tricholoma ustaloides.\n
\nAlthough Azad Jammu and Kashmir (AJK) have ample of medicinal plants to treat broad spectrum of ailments, there are many factors which are contributing for loss of ethnic flora e.g. over grazing, over exploitation, fire, deforestation etc. Lack of concern in the present generation has wiped out many rich wild flora of the area. It is necessary to create awareness about the usefulness of the flora. Cultivation of threatened medicinal plants should be encouraged by the local community in order to relieve pressure on wild plants. People should spread useful information on conservation and sustainable use of the natural resources of the area. There must be correct documentation, conservation of plants samples in herbarium of research institutes, and growing plants in gardens.
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