Escherichia coli

Authors: Johann Pitout

Previous authors: Allen C. Cheng, Nathan M. Thielman, MD, MPH, Richard L. Guerrant, MD

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History

In 1885 Theodor von Escherich described E. coli and named the organism Bacterium coli commune. Nine years later he noted its role as a human pathogen, and postulated that the organism was responsible for ascending urinary tract infections in young women (94).

EPIDEMIOLOGY

E. coli comprises of non-pathogenic commensal isolates that forms part of the normal flora of humans and various animals (96). In humans, they are the major aerobic organism residing in the intestine, typically with around 106 to 109 colony forming units per gram of stool (96). The organism is also found in soil and water, usually as a result of fecal contamination. Several variants or pathotypes of E. coli have been described that cause infections of the gastrointestinal system (i.e. intestinal pathogenic E. coli) while other pathotypes cause infections outside the gastrointestinal system (i.e. extraintestinal pathogenic E. coli) (13).

E. coli is the most common cause of urinary tract infections (UTIs) in humans (27), and is a leading cause of enteric infections and systemic infections (44). The systemic infections include bacteremia, nosocomial pneumonia, cholecystitis, cholangitis, peritonitis, cellulitis, osteomyelitis, and infectious arthritis. E. coli is also leading cause of neonatal meningitis (45).

MICROBIOLOGY, LABORATORY DIAGNOSIS AND TYPING

The organism is Gram-negative bacillus from the family Enterobacteriaceae that grows readily on simple culture media with minimal nutrients; glucose or glycerol is often sufficient. E. coli is typically first identified in the microbiology laboratory as a lactose-fermenting gram-negative rod that can grow both aerobically and anaerobically, preferably at 37ºC, and can be either non motile oo motile. It is oxidase negative, produces indole, does not ferment citrate, and demonstrates a positive methyl red test and a negative Voges-Proskauer reaction. The adoption of several molecular techniques has allowed for more rapid detection and identification of the different pathotypes (13).

E. coli can be typed according to their somatic lipopolysaccharide (O), capsular (K), and flagellar (H ) antigens. Classic serotyping is based on the Kauffman classification scheme where E. coli is typed using the O and H antigens(18). The O:H combination is referred to as a serotype. At least 174 O and 53 H antigen types have been described; however only a small subset of subset of O;H combinations are associated with human disease (Table 1). Most notable among these is E. coli O15;H7, one of the major serotypes seen in enterohemorrhagic E. coli infections. K1 encapsulated isolates constitute approximately 80% of E. coli causing neonatal meningitis (45).

While serotyping is informative for certain pathotypes (e.g. E. coli O15;H7), it is not always useful for other E. coli because some isolates are not type able using serotyping (18). Therefore, other methods have been developed to type E. coli for phylogenetic analysis, outbreaks and surveillance investigations (9). Pulsed field gel electrophoresis (PFGE) is still considered the gold standard for typing of E. coli during outbreak investigations (26, 90). This method is based on the specific digestion (or cutting) of bacterial DNA into fragments of varying sizes, followed by the separation of these DNA fragments into fingerprints by gel electrophoresis. PFGE is excellent for identifying different clones responsible for recent or on-going outbreaks. Unfortunately, PFGE is labor-intensive and time consuming and only delivers the best results when performed by a person with extensive technical experience in this method (90). Moreover, the comparison of data generated in different laboratories remains a challenge when using PFGE. Multilocus sequencing typing (MLST) is a sequence-based typing method that examines the nucleotide sequences of several (i.e. 6-10) housekeeping genes (57, 90). MLST is ideal for tracking and investigating antimicrobial resistant bacteria and their clones or sequence types (STs) to show common ancestry lineages among bacteria (56, 57). Unfortunately, MLST is expensive, time consuming and lacks the discrimination to investigate recent outbreaks. Next generation sequencing is an emerging technology with considerable promise for typing of medical important bacteria and yields all of the available DNA information in a single rapid step and provides a high-resolution, accurate and reproducible means that can be used for typing (4, 47).

PATHOGENESIS

The E. coli genome is composed of a conserved core of genes that provides the backbone of genetic information required for essential cellular processes and a flexible gene pool that harbours genetic information which provides properties (e.g. virulence and fitness genes) that enables the bacterium to adapt to special environmental conditions (22). The pathogenic ability of E. coli is largely afforded by the flexible gene pool through the gain and loss of genetic material (101, 104). Virulence factors involve mechanisms that enable pathogenic bacteria to cause infections and the presence to several putative virulence genes has been positively linked with the pathogenicity of E. coli.

Phylogenetic analyses have shown that E. coli falls into 5 main phylogenetic groups namely A, B1, B2, D and E (16). Extraintestinal pathogenic E. coli (ExPEC) belongs mainly to group B2 and, to a lesser extent, to group D while intestinal and commensal isolates tend to belong to groups A and B1.

Intestinal pathogenic E. coli include the following pathotypes: enteropathogenic E. coli (EPEC), enterohaemorrhagic E. coli (EHEC) [also referred to as Shiga-toxin producing E. coli (STEC)], enterotoxigenic E. coli(ETEC), enteroinvasive E. coli (EIEC including Shigella spp.), enteraggregative E. coli (EAEC) and diffusely adherent E. coli (DAEC) (14). Extraintestinal pathogenic E. coli (ExPEC) incorporates the following pathotypes; avian pathogenic E. coli (APEC), uropathogenic E. coli (UPEC), and those isolates responsible neonatal meningitis (NMEC) (46). Other pathotypes have also been identified but their mechanisms of pathogenesis are not well defined. The most interesting of the “other” pathotypes is referred to as adherent invasive E. coli (AIEC) that has been implicated in a subset of patients with Crohn’s disease (95). The different human E. colipathotypes, underlying virulence factors, clinical syndromes and treatment options are shown in Table 2.

CLINICAL INFECTIONS

E. coli is responsible for a wide variety of hospital and community-onset infections, affecting patients with normal immune systems as well as those with preexisting conditions (81). They often comprise the most common gram negative bacteria found in clinical laboratories including the vast majority of urinary, blood culture and peritoneal isolates. They may also be isolates from other sites including the respiratory tract, cerebrospinal fluid and various types of abscesses. Antimicrobial resistant isolates, especially those that are fluoroquinolone resistant and those producing extended-spectrum β-lactamases have increased significantly during the 2000’s and in certain areas many nosocomial and community-acquired E. coli are now resistant the several important antimicrobial classes (81).

Intestinal infections

Enteropathogenic E. coli (EPEC)

EPEC belongs to a group of E. coli collectively known as attaching and effacing pathogens based to their ability to form distinctive lesions on the surfaces of intestinal epithelial cells (49). The attachment and effacing of EPEC is due to a pathogenicity island known as the locus of enterocyte effacement (LEE). Typical EPEC isolates carry a large EPEC adherence factor plasmid that encodes for bundle-forming fimbriae (41). EPEC is a significant cause of infectious watery diarrhea that is often accompanied by fever, vomiting and dehydration in children under 2 years of age (52, 64). Persistent cases, lasting more than 2 weeks, have also been reported resulting in weight loss and malnutrition (64). Other clinical features include intolerance to cow’s milk and failure to respond to rehydration therapy. Detection included traditional O:H typing, fluorescent actin staining, tissue culture adherence assays, DNA probes and PCR based tests (71). In most cases, EPEC-induced diarrhea is self-limiting and can be effectively treated with oral rehydration therapy. Persistent infections may require the use of antimicrobials, however resistance to various agents have been reported (64, 71).

Enterohaemorrhagic E. coli (EHEC) [Shiga-toxin producing E. coli (STEC)]

The presence of Shiga toxin 1 or 2 genes, typically acquired by a bacteriophage, qualifies an E. coli as a Shiga toxin producing E. coli (STEC) (23). These isolates are also referred to as verotoxin-producing E. coli(VTEC). Enterohaemorrhagic E. coli (EHEC) is a subset of STEC that was originally described by its association with hemorrhagic colitis (67). EHEC is often LEE positive and forms similar attachment and effacing lesions as EPEC (49). The most common EHEC serogroup is O157:H7 and this serogroup had been responsible for various world-wide outbreaks of infection (34). Of interest, STEC O104:H4, that was recently responsible for major outbreaks of hemorrhagic colitis (HC) and haemolytic uremic syndrome (HUS) in Europe (especially in Germany), can be considered as a hybrid of EHEC and enteraggregative E. coli (EAEC) (39).Infections with STEC can range from mild watery diarrhea to bloody diarrhea (hemorrhagic colitis) and the risk of HUS. The first symptom is usually watery diarrhea followed by fever, abdominal cramping and vomiting (24). Both O157 and non-O157 STEC can have similar clinical presentations; however, O157 has higher rates of complications such as HC and HUS (24,67). Most O157:H7 are unable to ferment sorbitol within a 24 hour period and sorbitol MacConkey and chromogenic media had been used to detect this serogroup (35, 71). Shiga toxins can be detected with enzyme immunoassay (EIA) and PCR techniques; these tests can also be directly performed on stool specimens that will ensure the additional detection of non-O157 isolates (35, 71). The course of infection is usually self-limiting and resolves within 7 days. Treatment of infection is mostly supportive and the use of antibiotics is not recommended (17). Currently there is no way to prevent the development of HUS following STEC infection. Alternative treatment modalities such as the use of monoclonal antibodies are ongoing (17).

Enterotoxigenic E. coli (ETEC)

ETEC is a major cause of traveler’s diarrhea and is endemic in most underdeveloped countries with significant mortality rates in children (36). ETEC is defined by its ability to produce either heat stable (LT) or heat-labile (ST) enterotoxins and it also carries various colonization factors for adherence to the intestinal epithelium. The genes encoding for the toxins and adherence factors are often found on plasmids (36). ETEC causes mild to severe watery diarrhea that has a clinical presentation very similar to cholera and can rapidly lead to dehydration (66). The diarrhea is sometimes accompanied by fever, abdominal cramping and vomiting that lasts about 3 to 5 days. The diagnosis of ETEC infections is made via the detection of LT and ST enterotoxins with molecular methods such as PCR or DNA probes (71). ETEC-associated diarrhea is self-limiting and oral rehydration with the maintenance of fluid and electrolyte balance is very effective for children and adults (66). The parenteral route might be indicated in severe cases of dehydration. Anti-motility drugs such as loperamide and antibiotics are useful to treat cases of traveler’s diarrhea (3 3). As with EPEC, resistance to various antimicrobial agents has also been noted among ETEC.

Enteroinvasive E. coli (EIEC)

EIEC and Shigella spp are the etiological agents of bacillary dysentery (also called shigellosis).Serotype classification provides the basis for the current EIEC and Shigella nomenclature. However, phylogenetic studies have demonstrated that Shigella clearly belongs to the species E. coli (51). EIEC, like Shigella, contain a plasmid that enables the bacteria to invade epithelial cells, suppress the host immune response and spread directly from cell to cell (10, 74). EIEC in general terms, cause less severe disease than Shigella spp (102). The clinical presentation of EIC consists of mild watery diarrhea, fatigue, malaise, fever and anorexia during the early stages of infection. This is followed by dehydration, abdominal cramps, tenesmus, stools with blood and mucus (102). In most cases, the infection is self-limiting. However, severe life threatening complications can occur including megacolon, intestinal perforation, peritonitis, pneumonia and HUS. EIEC isolates are detected in culture as lactose negative colonies and confirmed by DNA probes or PCR for virulence associated genes (71). Mild to moderate infections are normally self-limiting and proper rehydration remains the mainstay for therapy in such cases. Antimicrobial therapy has proven to shorten duration of symptoms and reduce the risk of serious complications (77). Recommended antibiotics include azithromycin, cefixime, ceftriaxone, ciprofloxacin and levofloxacin. As with EPEC and ETEC, resistance to various antimicrobial agents has also been noted among EIEC.

Enteraggregative E. coli (EAEC)

EAEC was identified as a cause of infection during the 1980s and is defined by the aggregative patterns of adherence to tissue culture cells (65). EAEC causes persistent diarrhea in children from endemic areas, as well as persistent diarrhea in patient infected with HIV and is an important causative agent of traveler’s diarrhea. Several types of aggregative fimbrial adhesins and enterotoxins play important roles in the pathophysiology of the disease. Infections due to EAEC often presents with watery diarrhea with mucus that can be accompanied by fever, vomiting, and abdominal pain. Persistent infections can lead to significant weight loss and malnutrition in children from endemic areas (25). Laboratory diagnosis remains a challenge because of the heterogeneity of EAEC isolates (71). EAEC-induced diarrhea can be treated with oral rehydration therapy and persistent infections may require the use of antimicrobials (25, 71). Antibiotics such a fluorquinolones are useful to treat cases of traveler’s diarrhea (33). However, antimicrobial resistance is increasing among EAEC in certain parts of the world.

Diffusely adherent E. coli (DAEC)

DAEC describes E. coli isolates that cause diarrhea by attaching to epithelial cells but do not fall in the classical patterns of adherence (3). Some researchers consider them as distinct from other pathotypes but because of difficulties in classification and identification of DAEC, the exact role of this pathotype requires additional epidemiological studies.

Extraintestinal infections

Extraintestinal pathogenic E. coli (ExPEC), especially the uropathogenic E. coli (UPEC) pathotype, is most commonly associated with human infections due to E. coli outside the intestinal tract (46). UPEC are important causes of lower urinary tract infections (UTIs) and systemic infections in humans (81). The systemic infections include upper UTIs, bacteremia, nosocomial pneumonia, cholecystitis, cholangitis, peritonitis, cellulitis, osteomyelitis, infectious arthritis (28). ExPEC is also leading cause of neonatal meningitis (referred to as NMEC) (45). ExPEC isolates exhibit considerable genome diversity and possess a broad range of virulence-associated factors, including toxins, adhesions (especially type I and p fimbrae), lipopolysaccharides, polysaccharide capsules, proteases and invasins, which are frequently encoded by genes in pathogenic islands or other mobile DNA islands (21). It seems that these putative virulence factors contribute to fitness (e.g. iron-uptake systems, bacteriocins, proteases, adhesins) of ExPEC and increase the adaptability, competitiveness and ability to colonize the human body, rather than being typical virulence factors directly involved in infection (81). Several virulence factors such as type 1 fimbrae, the K1 capsule, and several cytotoxic factors play important roles in the ability of NMEC to cause meningitis (45).

UPEC is the primary causes of community-acquired UTIs, with an estimated 20% of women over the age of 18 years suffering from an UTI during their lifetime (27). UPEC is responsible for 70-95% of community-onset UTIs and approximately 50 % of nosocomial UTIs, hence accounting for substantial morbidity, mortality and medical expenses (61, 62). UPEC is the most common cause of uncomplicated and complicated UTIs (61, 62). Recurrent or relapsing UTIs are especially problematic in many individuals. The primary reservoir of UPEC is believed to be the human intestinal tract and isolates act as opportunistic pathogens that employ diverse repertoire of virulence factors to colonize and infect the urinary tract in an ascending fashion (27, 28). However, community-onset clonal outbreaks of UTIs, possibly due to the consumption of food contaminated with UPEC have also been described (28). Additionally, there is some evidence that UPEC isolates can also be transmitted via sexual activities (28).

Antimicrobial therapy remains the cornerstone for treating infections due to ExPEC. The b-lactam antibiotics, especially the 3rd generation cephalosporins, and the fluroquinolones are the major drug classes used to treat serious community-onset or hospital-acquired infections caused by ExPEC (79, 81, 93).

ANTIMICROBIAL RESISTANCE

Antimicrobials used to treat infections due to E. coli

A wide range of antimicrobial agents effectively inhibit the growth of E. coli. The β-lactams, fluoroquinolones, aminoglycosides and trimethoprim-sulfamethoxazole are often used to treat community and hospital infections due to E. coli (81). β-lactams disrupt cell wall synthesis by binding to and inhibiting the penicillin-binding proteins essential for transpeptidation and carboxypeptidation reactions in cell wall peptidoglycan synthesis. Fluoroquinolones interfere with DNA supercoiling and promote DNA gyrase-mediated double-stranded DNA. The aminoglycosides bind irreversibly to the 50S subunit of the 70S bacterial ribosomes. Sulfonamides and trimethoprim interfere with bacterial folic acid synthesis by inhibiting tetrahydropteric acid syntheses and dihydrofolate reductase, respectively.

Resistance to antimicrobial agents

The b-lactam antibiotics, especially the cephalosporins and b-lactam-b-lactamases inhibitor combinations, are major drug classes used to treat community-onset or hospital-acquired infections caused by E. coli,especially due to the ExPEC pathotype (80). Among E coli, b-lactamase production remains the most important contributing factor to b-lactam resistance. b-lactamases are bacterial enzymes that inactivate b-lactam antibiotics by hydrolysis, which results in ineffective compounds (38).

Resistance to aminopenicillins (e.g. ampicillin) and early-generation cephalosporins (e.g. cefazolin) among E. coli is often mediated by the production of narrow-spectrum b-lactamases such as TEM-1, TEM-2 and to a lesser extent SHV-1 enzyme (5). Most importantly among E. coli, is the increasing recognition of isolates producing the so-called “newer b-lactamases” that causes resistance to the expanded-spectrum cephalosporins and/or the carbapenems. These enzymes consist of the plasmid-mediated AmpC b-lactamases (e.g. CMY types), extended-spectrum b-lactamases (e.g. TEM, SHV, CTX-M types), and carbapenemases (KPC types, metallo-b-lactamases (MBLs) and OXA-types) (5, 63). CMY, CTX-M, and NDM types of b-lactamase are mostly responsible for the emerging resistance to the β-lactam antibiotics among E. coli (81). The characteristics of these newer b-lactamases including the KPC and OXA types are summarized in Table 3. The VIM, IPM, KPC and OXA-48 β-lactamases had been described in various members of the Enterobacteriaceae (especiallyKlebsiella spp.) and are not yet commonly encountered among E. coli.

The up regulation of efflux pumps and plasmid-mediated resistance mechanisms (e.g. qnr determinants) can reduce fluoroquinolone susceptibilities in E. coli, however high level resistance to the fluoroquinolones typically requires 1-2 point mutations within the quinolone resistance determining regions of gyrA and parC, the chromosomal genes encoding for DNA gyrase and topoisomerase IV respectively (42).

Resistance to aminoglycosides may develop because of impaired uptake and aminoglycoside phosphorylation, although enzymatic modification by acetylation of an amino group is considered the most common mechanism. The genes encoding for enzymatic modification of aminoglycosides are often part of class I integrons (30). A variant of aminoglycoside acetyltransferase aac(6’)-Ib , named aac(6’)-Ib-cr are very prevalent among antibiotic resistant E. coli (69). AAC(6’)-Ib-cr has the additional ability to acetylate fluoroquinolones with unprotected amino nitrogen on the piperazine ring that includes norfloxacin and ciprofloxacin.

Trimethoprim-sulfamethoxazole resistance results from alterations of different substrate enzymes or their overproduction, loss of bacterial drug-binding capacity, and decreased cell permeability.

Emerging Trends in Resistance among E. coli

E. coli, especially the ExPEC pathotype, is an important cause of community and nosocomial-acquired infections, especially of urinary tract infections, bloodstream infections, surgical site infections, pneumonia and sepsis (81).The cephalosporins, fluoroquinolones, and trimethoprim-sulfamethoxazole are considered as 1st line agents and often used to treat community and hospital infections caused by E. coli. The management of infections caused by ExPEC has been complicated by the emergence of antimicrobial resistance to first line antibiotics (84). Until the late 1990s, ExPEC were relatively susceptible to 1st line antibiotics, however severalsurveillance studies during the 2000’s across Europe, North and South America, have shown that between 20 – 55% of ExPEC are resistant to 1st line antibiotics including the cephalosporins, fluoroquinolones, and trimethoprim-sulfamethoxazole (81, 84, 93). Resistance to these agents is causing delays in appropriate therapy with subsequent increased morbidity and mortality (92, 100).

Extended-spectrum β-lactamases

The most well-known of the “newer” β-lactamases was first described in 1983 and have been named the extended-spectrum β-lactamases or ESBLs. These enzymes have the ability to hydrolyse the penicillins, cephalosporins and monobactams, but not the cephamycins and carbapenems. ESBLs are inhibited by “classical” b-lactamase inhibitors such as clavulanic acid, sulbactam and tazobactam (Table 3) (70). Although ESBLs have been identified in a range of Enterobacteriaceae, they are most often present in E. coli and K. pneumoniae. The majority of ESBLs identified in clinical isolates during the 1980s to 90s were of the SHV or TEM types, which evolved from parent enzymes such as TEM-1, -2 and SHV-1. A different type of ESBL, named CTX-M b-lactamases, originated from environmental Kluyvera spp, and gained prominence in the early 2000s with reports of clinical isolates of E. coli producing these enzymes from Europe, Africa, Asia, South and North America (85). Since the mid 2000’s, the prevalence of CTX-M β-lactamases increased significantly inE. coli from various parts of the world, and today have become the most wide-spread and common type of ESBL (85).

CTX-M-producing E. coli are important causes of community-onset urinary tract infections, bacteraemia and intra-abdominal infections (85). Risk factors associated with infections caused by CTX-M-producing E. coliinclude the following: repeat UTIs, underlying renal pathology, previous antibiotics including cephalosporins and fluoroquinolones, previous hospitalization, nursing home residents, older males and females, Diabetes Mellitus, underlying liver pathology and international travel to high risk areas such as the Indian subcontinent (89). Surveys from several countries worldwide have illustrated an alarming trend of associated resistance to other classes of antimicrobial agents among CTX-M-producing E. coli that included trimethoprim-sulfamethoxazole, tetracycline, gentamicin, tobramycin and ciprofloxacin (85). Studies consistently show that infections due to ESBL-producing Enterobacteriaceae are associated with a delay in initiation of appropriate antibiotic therapy, which consequently prolongs hospital stays and increases hospital costs (92). More importantly, failure to initiate appropriate antibiotic therapy from the start appears to be responsible for higher patient mortality (100).

Currently, the most widespread and prevalent type of CTX-M enzyme among human clinical isolates of E. coli is CTX-M-15 (15). In 2008, E. coli sequence type (ST) ST131 with CTX-M-15 was simultaneously identified in nine countries, spanning three continents (12, 60). The intercontinental dissemination of this ST since then, has contributed immensely to the worldwide emergence of fluoroquinolone resistant and CTX-M-15 producing E. coli (72). Recent surveys have shown that ST131 accounted for over 50% of fluroquinolone-resistant or ESBL-producing E. coli (11, 40, 75). A recent study from Canada that investigated the molecular epidemiology of ESBLs-producing E. coli causing bacteraemia over an 11-year period (2000-10), showed that ST131 was the most common and antimicrobial resistant sequence type, and the influx of a single pulsotype of ST131, was responsible for a significant increase since 2007 of ESBL-producing E. coli (76).

Johnson and colleagues investigated the presence and virulence properties of ST131 among 127 E. coli from the 2007 SENTRY and Meropenem Yearly Susceptibility Test Information Collection (MYSTIC) surveillance programs across the United States (40). Overall 54 (i.e. 17%) belonged to ST131, but interestingly, this ST included 52% of isolates that showed resistance to > 3 antimicrobial classes. ST131 has a significant higher virulence score that other ExPEC, and the presence of certain virulence factors were associated with this sequence type. Their results showed that ST131 had distinctive virulence and resistance profiles, and concluded that the combination of antimicrobial resistance and certain virulence factors, may be responsible for the epidemiological success of this sequence type. Whole genome sequencing of 105 ST131 isolates from 5 countries revealed that fluoroquinolone resistance was confined to a single, rapidly expanding sublineage designated H30-R (86). Interestingly, H30-R with CTX-M-15 belonged to a single, well-defined clade nested within other H30-R isolates and was named H30-Rx due to its more extensive resistance to antimicrobial agents.

Plasmid-mediated AmpC-b-lactamases

Escherichia coli possess a chromosomal gene that encodes for an AmpC β-lactamase. Usually, low amounts of these β-lactamases are produced because the AmpC gene is regulated by a weak promoter and a strong attenuator system (38). Occasionally, cephamycin and/or cephalosporin-resistant E. coli are encountered that produce plasmid-mediated β-lactamases, derived from bacteria with chromosomally encoded AmpC-cephalosporinases (78). E. coli that produce plasmid-mediated or imported AmpC b-lactamases were first reported in the 1980's. These enzymes (e.g. CMY, ACT, FOX, ACT, and DHA types) are derivatives of the chromosomally encoded AmpC cephalosporinases of bacteria such as Enterobacter spp., C. freundii, M. morganii, Aeromonas spp. and Hafnia alvei and are not inhibited by the “classical” b-lactamase inhibitors such as clavulanic acid, sulbactam and tazobactam (38) (Table 3). However, different types of inhibitors such as boronic acid and cloxacillin have the ability to inhibit chromosomal and plasmid-mediated AmpC b-lactamases (Table 3) (97). Resistance to the fourth generation cephalosporins (e.g. cefepime) are caused by point mutations in AmpC β-lactamases and is called extended-spectrum cephalosporinases (38). The genes are typically encoded on large plasmids containing additional antibiotic resistance genes that are responsible for multi-resistant phenotype, leaving few therapeutic options (32).

A survey from five children’s hospitals in China, detected AmpC b-lactamases in 10% of K. pneumoniae (64/637), in 2% of E. coli (10/494) with an overall increase from 2005 (2.6%) to 9.3% in 2006 (20). A multicenter survey from 63 hospitals conducted in the USA detected transferable AmpC b-lactamases in 3.3% of K. pneumoniae isolates at 16 of the 63 sites (25%) with no difference between ICU and non-ICU sites (58). The SENTRY Antimicrobial Surveillance Program in the USA found plasmid-mediated AmpC b-lactamases in 2% of 1429 E. coli isolates from 30 centers; with CMY-2, FOX-5 and DHA-1 being identified (19).

It seems that CMY-2 (stands for active on CephaMYcins) is the most common imported AmpC b-lactamase reported in Enterobacteriaceae from different areas of the world (38). Jacoby and colleagues found plasmid-mediated AmpC-type resistance in 7 of 75 of ceftazidime resistant E. coli from 25 U.S. states; 2 of these isolates produced CMY-2 (2). Mulvey and colleagues studied 232 cefoxitin resistant E. coli from 12 different hospitals in Canada and found 25 (11%) strains contained CMY-2 and 51 (22%) had different promoter and attenuator mutations (59). Hospital surveys from Asia, North America and Europe have shown that the DHA types of cephamycinases are mostly present in Klebsiella spp from Asia, CMY are present in E. coli from Asia, North American and Europe while FOX are present in Klebsiella spp. from North America and Europe (38).

Just like ESBL-producing bacteria, organisms with plasmid-mediated AmpC enzymes have mostly been responsible for nosocomial outbreaks on a worldwide basis especially during the late 1980’s and 1990’s (38). Analysis of these outbreaks had shown that increased length of hospital stay, severity of illness, admission to an intensive care unit (ICU), and previous exposure to antibiotics are associated with infections with plasmid-mediated AmpC b-lactamase producing Enterobacteriaceae. In a study reported by Pai et al from Korea, bloodstream infections caused by plasmid-mediated AmpC-producing (i.e. DHA-1 and CMY-1) K. pneumoniaehad similar clinical features, risk factors and outcomes to those patients infected with TEM- or SHV-related ESBL producers (68). All the patients that received an extended-spectrum cephalosporin (i.e. cefotaxime, ceftazidime, ceftriaxone) had failed therapy.

A population-based study from the Canada has identified AmpC-producing E. coli in 61% of 369 patients with community-associated infections due to cephamycin-resistant isolates and found that women were at five-times higher risk for developing an infection (83). PCR showed that 125 (34%) were positive for blacmy genes and sequencing identified these enzymes to be CMY-2. The study concluded that in this large Canadian region, AmpC-producing E. coli is an emerging pathogen in the community that commonly causes urinary tract infections in older women. This was followed by 2 reports from Washington and Nebraska respectively that showed Enterobacteriaceae that produce CMY, ACC and DHA types of AmpC b-lactamases are present in outpatient clinics in the USA (31, 87).

Metallo-β-lactamases (e.g. NDM-1)

The production of MBLs of the IMP and VIM types, have mostly been detected in P. aeruginosa and remain relatively rare in members of the Enterobacteriaceae except for K. pneumoniae and E. coli present in Mediterranean Europe (VIM-producing K. pneumoniae in Greece, Italy and Spain), and Taiwan and Japan (IMP-producing E. coli) (6). IMP and VIM types of MBLs are often associated with class 1 integrons that contain various gene cassettes that often render isolates resistant to various groups of antimicrobial agents.

Recently, a new type of metallo-β-lactamase (MBL), named NDM, was described in K. pneumoniae and E. coli recovered from a Swedish patient who was hospitalized in New Delhi, India. MBLs have the ability to hydrolyse a wide variety of b-lactams, including the penicillins, cephalosporins and carbapenems, but not the monobactams (i.e. aztreonam), and are inhibited by metal chelators such as EDTA (43) (Table 3). The majority of NDM-1-producing bacteria are broadly resistant to various drug classes and also carry a diversity of other resistance mechanisms (e.g. to aminoglycosides and fluoroquinolones), which leaves limited treatment options.

Kumarasamy and colleagues (48), provide compelling evidence that NDM-producing Enterobacteriaceae (mostly K. pneumoniae and E. coli) are widespread in India and Pakistan. They also found that many UK patients infected with NDM-producing bacteria had recently traveled to India to undergo several types of medical procedures. The patients presented with a variety of hospital- and community-associated infections with urinary tract infections (UTIs) being the most common clinical syndrome. Recent reports from the subcontinent (including India, Pakistan and Bangladesh) show that the distribution of NDM β-lactamases among Enterobacteriaceae are widespread through these countries (7, 8, 53).

Since 2011, NDM-1-positive bacteria have been reported worldwide (43). Most are Enterobacteriaceae including E. coli from patients hospitalized in 2009 and 2010 with an epidemiological link to the Indian subcontinent. Recent findings suggest that the Balkan states and the Middle East might act as secondary reservoirs for the spread of NDM-1, which may or may not initially have reached these countries from the Indian subcontinent (43). Enterobacteriaceae with NDM-1 have been recovered from many clinical settings, reflecting the disease spectra of these opportunistic bacteria, including hospital and community-onset urinary tract infections, septicemia, pulmonary infections, peritonitis, device-associated infections and soft tissue infections. NDM-1-positive bacteria have been recovered from the gut flora of travelers returning from the Indian subcontinent and undergoing microbiological investigation for unrelated diarrheal symptoms (55). There is also widespread environmental contamination by NDM-1-positive bacteria in New Delhi (103).

There is no evidence that E. coli that produce NDM are more virulent than other isolates, however recent studies described presence of NDM β-lactamases in the very successful E. coli ST131 with an identical virulence genotype than ST131 that produce CTX-M β-lactamases (78). Of interest, ST131 with VIM, KPC, OXA-48 carbapenemases have also recently been described (43). Due to the very resistant nature of these NDM-producing E. coli, the treatment of infections due to these bacteria will remain a challenge to physicians. Antibiotics such as colistin, tigecycline and fosfomycin show the best activity against NDM-producing bacteria (1).

ANTIMICROBIAL THERAPY

Drugs of Choice

Despite the concerning trends in antimicrobial resistance among E. coli isolates worldwide, a growing armamentarium of antimicrobial agents provides multiple options for treating E. coli infections. Ironically, these newer agents are more readily available and affordable in developed nations where E. coli resistance is less of a problem, compared to the developing world. As with other Enterobacteriaceae, where and when available, antimicrobial testing of the infecting strain should direct therapy. In other situations, knowledge of recent local susceptibility patterns is useful for guiding treatment. In general, monotherapy with trimethoprim-sulfamethoxazole, aminoglycoside, cephalosporin, or a fluoroquinolones is recommended as the treatment of choice for most known infections with E. coli, although many broad spectrum agents (such as ß-lactam/ß-lactamase inhibitor combinations and the carbapenems) remain highly active.

Treatment of infections due to multi-resistant E. coli

The presence of ESBLs and AmpC b-lactamases complicates antibiotic selection especially in patients with serious infections such as bacteraemia. The reason for this is that these bacteria are often multiresistant to various antibiotics and an interesting feature of CTX-M-producing isolates is the co-resistance to the fluoroquinolones (84). Antibiotics that are regularly used for empiric therapy of serious community-onset infections, such as the third generation cephalosporins or fluoroquinolones are often not effective against ESBL and or AmpC-producing bacteria (82). This multiple drug resistance has major implications for selection of adequate empiric therapy regimens. Empiric therapy is prescribed at the time when an infection is clinically diagnosed while awaiting the results of cultures and anti-microbial susceptibility profiles. Multiple studies in a wide range of settings, clinical syndromes, and organisms have shown that failure or delay in adequate therapy results in an adverse mortality outcome. This is also true of infections caused by ESBL-producing bacteria (92). A major challenge when selecting an empiric regimen is to choose an agent that has adequate activity against the infecting organism(s). Empirical antibiotic choices should be individualized based on institutional antibiograms that tend to be quite different from hospital to hospital, city to city and country to country.

The carbapenems are widely regarded as the drugs of choice for the empiric treatment of severe infections due to AmpC- and ESBL-producing E. coli (81). It is reasonable to suggest that ertapenem should be used for serious community-onset infections in cases where ESBL-producing isolates are suspected to be the source (80). This would include patient with the following risk factors (89); repeat UTIs, underlying renal pathology, recent administration of previous antibiotics (including cephalosporins and fluoroquinolones), previous hospitalization, nursing home residents, older males, Diabetes Mellitus, underlying liver pathology and recent international travel to high risk areas (e.g. the Indian subcontinent) (54). Imipenem or meropenem or doripenem would be more appropriate for the empiric treatment of serious hospital-onset infections in cases where ESBL-producing isolates are suspected to be the source (80). The existing data mostly from Spain suggest that piperacillin-tazobactam may be a useful agent for the treatment of some infections with ESBL-producing pathogens (88) . At the present time, however, this potential recommendation must be interpreted cautiously, because it is based on a relatively small database of information. Definitive conclusions regarding the efficacy of piperacillin-tazobactam for the treatment of infections caused by E. coli that produce ESBLs must await large-scale, prospective, randomized clinical trials.

Oral agents such as nitrofuratoin, and fosfomycin show good in-vitro activity against ESBL and AmpC-producing from different areas of the world and are adequate options for the empiric treatment of uncomplicated lower UTIs (80). However, it is important for medical practitioners to know their local susceptibility rates for nitrofuratoin against these multi-resistant bacteria, since in certain areas high resistance rates had been reported.

Other agents such as temocillin, pivmecillinam and colistin show good in-vitro activity against ESBL-producing bacteria especially if present in E. coli (99, 105). The clinical and bacteriological efficacy of pivmecillinam against lower UTIs caused by ESBL-producing E. coli and K. pneumoniae showed good clinical activity but the bacteriological cure rates were low (98). A recent study investigated the in-vitro activity of mecillinam-clavulanate combination against ESBL-producing bacteria that showed that the addition of clavulanate did improve the activity of mecillinam, even when high bacterial inoculums were present (50).

Antimicrobial options for the treatment of infections caused by E. coli that produce ESBLs, and AmpC b-lactamases are summarized in Tables 4, and 5.

Due to the very resistant nature of E. coli that produce carbapenemases, the treatment of infections due to these bacteria will remain a challenge to physicians. Clinical studies of antimicrobial therapy and the outcome of patients infected with carbapenemase-producing E. coli, compared with patients infected with susceptible strains, are very limited and suggest worse clinical outcomes for patients with infections due to resistant isolates (91). Antibiotics such as colistin, tigecycline, temocillin and fosfomycin show the best in-vitro activity against carbapenemase-producing E. coli. Unfortunately clinical evaluations have provided limited evidence for improved outcome when these agents are used (29).

Treatment of syndromes caused by E. coli

The reader is referred to those specific chapters (e.g. urinary tract infections, gastro-intestinal infections).

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