Susceptibility of enterococci and epidemiology of enterococcal infection in the 1980s

CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis

Enterococcus faecalis is a bacterium that normally inhabits the gastrointestinal tracts of humans and other animals. Although these bacteria are members of our native gut flora, they can cause life-threatening infections in hospitalized patients. Antibiotic resistance genes appear to be readily shared among high-risk E. faecalis strains, and multidrug resistance in these bacteria limits treatment options for infections. Here, we find that CRISPR-Cas and restriction-modification systems, which function as adaptive and innate immune systems in bacteria, significantly impact the spread of antibiotic resistance genes in E. faecalis populations. The loss of these systems in high-risk E. faecalis suggests that they are immunocompromised, a tradeoff that allows them to readily acquire new genes and adapt to new antibiotics.

Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial infections. Conjugative pheromone-responsive plasmids are narrow-host-range mobile genetic elements (MGEs) that are rapid disseminators of antibiotic resistance in the faecalis species. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification confer acquired and innate immunity, respectively, against MGE acquisition in bacteria. Most multidrug-resistant E. faecalis isolates lack CRISPR-Cas and possess an orphan locus lacking cas genes, CRISPR2, that is of unknown function. Little is known about restriction-modification defense in E. faecalis. Here, we explore the hypothesis that multidrug-resistant E. faecalis strains are immunocompromised. We assessed MGE acquisition by E. faecalis T11, a strain closely related to the multidrug-resistant hospital isolate V583 but which lacks the ~620 kb of horizontally acquired genome content that characterizes V583. T11 possesses the E. faecalis CRISPR3-cas locus and a predicted restriction-modification system, neither of which occurs in V583. We demonstrate that CRISPR-Cas and restriction-modification together confer a 4-log reduction in acquisition of the pheromone-responsive plasmid pAM714 in biofilm matings. Additionally, we show that the orphan CRISPR2 locus is functional for genome defense against another pheromone-responsive plasmid, pCF10, only in the presence of cas9 derived from the E. faecalis CRISPR1-cas locus, which most multidrug-resistant E. faecalis isolates lack. Overall, our work demonstrated that the loss of only two loci led to a dramatic reduction in genome defense against a clinically relevant MGE, highlighting the critical importance of the E. faecalis accessory genome in modulating horizontal gene transfer. Our results rationalize the development of antimicrobial strategies that capitalize upon the immunocompromised status of multidrug-resistant E. faecalis.

IMPORTANCEEnterococcus faecalis is a bacterium that normally inhabits the gastrointestinal tracts of humans and other animals. Although these bacteria are members of our native gut flora, they can cause life-threatening infections in hospitalized patients. Antibiotic resistance genes appear to be readily shared among high-risk E. faecalis strains, and multidrug resistance in these bacteria limits treatment options for infections. Here, we find that CRISPR-Cas and restriction-modification systems, which function as adaptive and innate immune systems in bacteria, significantly impact the spread of antibiotic resistance genes in E. faecalis populations. The loss of these systems in high-risk E. faecalis suggests that they are immunocompromised, a tradeoff that allows them to readily acquire new genes and adapt to new antibiotics.

Antimicrobial Susceptibility Patterns of Enterococcus faecalis and Enterococcus faecium Isolated from Poultry Flocks in Germany

Between 2010 and 2011, 145 Enterococcus isolates (Enterococcus faecalis, n = 127; Enterococcus faecium, n = 18) were collected during routine bacteriologic diagnostics from broilers, layers, and fattening turkeys in Germany showing various clinical signs. The susceptibility to 24 antimicrobial agents was investigated by broth microdilution test to determine minimum inhibitory concentrations (MICs). All E. faecalis isolates (n = 127) were susceptible to the beta-lactam antibiotics ampicillin, amoxicillin-clavulanic acid, and penicillin. Corresponding MIC with 50% inhibition (MIC50) and MIC with 90% inhibition (MIC90) values of these antimicrobial agents were at the lower end of the test range (≤ 4 μg/ml). In addition, no vancomycin-resistant enterococci (VRE) were found. High resistance rates were identified in both Enterococcus species for lincomycin (72%-99%) and tetracycline (67%-82%). Half or more than half of Enterococcus isolates were resistant to gentamicin (54%-72%) and the macrolide antibiotics erythromycin (44%-61%) and tylosin-tartate (44%-56%). Enterococcus faecalis isolated from fattening turkeys showed the highest prevalence of antimicrobial resistance compared to other poultry production systems. Eighty-nine out of 145 Enterococcus isolates were resistant to three or more antimicrobial classes. Again, turkeys stood out with 42 (8 1%) multiresistant isolates. The most-frequent resistance patterns of E. faecalis were gentamicin, lincomycin, and tetracycline in all poultry production systems.

Surveillance of antimicrobial resistance at a tertiary hospital in Tanzania

BACKGROUND

Antimicrobial resistance is particularly harmful to infectious disease management in low-income countries since expensive second-line drugs are not readily available. The objective of this study was to implement and evaluate a computerized system for surveillance of antimicrobial resistance at a tertiary hospital in Tanzania.

METHODS

A computerized surveillance system for antimicrobial susceptibility (WHONET) was implemented at the national referral hospital in Tanzania in 1998. The antimicrobial susceptibilities of all clinical bacterial isolates received during an 18 months' period were recorded and analyzed.

RESULTS

The surveillance system was successfully implemented at the hospital. This activity increased the focus on antimicrobial resistance issues and on laboratory quality assurance issues. The study identified specific nosocomial problems in the hospital and led to the initiation of other prospective studies on prevalence and antimicrobial susceptibility of bacterial infections. Furthermore, the study provided useful data on antimicrobial patterns in bacterial isolates from the hospital. Gram-negative bacteria displayed high rates of resistance to common inexpensive antibiotics such as ampicillin, tetracycline and trimethoprim-sulfamethoxazole, leaving fluoroquinolones as the only reliable oral drugs against common Gram-negative bacilli. Gentamicin and third generation cephalosporins remain useful for parenteral therapy.

CONCLUSION

The surveillance system is a low-cost tool to generate valuable information on antimicrobial resistance, which can be used to prepare locally applicable recommendations on antimicrobial use. The system pinpoints relevant nosocomial problems and can be used to efficiently plan further research. The surveillance system also functions as a quality assurance tool, bringing attention to methodological issues in identification and susceptibility testing.

The prevalence of faecal carriage of ampicillin-resistant and high-level gentamicin-resistant enterococci among inpatients at 10 major Norwegian hospitals

From March to October 1999, 854 patients hospitalized at 10 major Norwegian hospitals were screened for rectal carriage of ampicillin-resistant enterococci (ARE) and high-level gentamicin-resistant enterococci (HLGRE). A total of 59 ARE carriers (prevalence 6.9%, range 0-22% among hospitals) and 28 HLGRE carriers (prevalence 3.3%, range 1-11%) were detected. All ARE or HLGRE strains were susceptible to vancomycin, whereas 77% of the ARE isolates were resistant to ciprofloxacin. All the ARE strains were identified as Enterococcus faecium, and 48% of these were genomically closely related as shown by PFGE. Specific point mutations in the pbp5 gene were associated with reduced susceptibility to ampicillin. The adjusted risk of becoming a carrier of ARE was related to the use of glycopeptides [odds ratio (OR) = 4.8], the use of any antimicrobial agent (OR = 3.1) and more than one hospital admission during the last six months (OR = 2.0). Twenty-five of 28 HLGRE isolates were Enterococcus faecalis. The aacA/aphD genes were detected in 26 (93%) and the aphA3 in 19 (68%) of the HLGRE isolates. Sixty-four percent of the HLGRE isolates belonged to two PFGE clusters. Consumption of antimicrobial agents was also a significant risk factor for HLGRE colonization (OR = 5.4), while prescription of penicillins was associated with reduced risk (OR = 0.28).

Nosocomial outbreak of ampicillin resistant Enterococcus faecium: risk factors for infection and fatal outcome

A nosocomial outbreak caused by ampicillin resistant Enterococcus faecium (ARE) was detected at a Norwegian university hospital in January 1995. Prior to this outbreak, ARE were not common in this hospital or other hospitals in Norway. During 1995 and 1996, a total of 149 cases with clinical ARE infection were detected prospectively. A case control study was performed by allocating controls matched for gender, age and ward of admission. Altogether, 123 case control pairs with mean age 70.1 years were included. Isolates from 89 (72. 4%) of the cases were identical or related to the defined outbreak strain as determined by pulsed-field gel electrophoresis (PFGE). In 75 of the patients (60.9%), ARE caused urinary tract infection, five (4.1%) had bacteraemia, 33 (26.8%) had wound infection and 10 (8.1%) had other infections. In a logistic regression model for 1:1 matched samples, the following factors were identified as significant risk factors for ARE infection: underlying neurological disease (OR=33.5), prescription of antimicrobial agents for more than 10 days (OR=8. 99), prescription of cephalosporins (OR=4.69), underlying gastrointestinal disease (OR=3.36) and length of hospital stay per day (OR=1.04). The intrahospital death rate for the cases was 18.7% compared with 8.9% for the controls, corresponding to an excess mortality attributable to ARE infection of 9.8%. A history of carbapenem prescription was the only independent factor contributing to death (OR=5.64) when comparing ARE patients dying in hospital to those surviving.

First confirmed case of a vancomycin-resistant Enterococcus faecium with vanA phenotype from Brazil: isolation from a meningitis case in São Paulo

The importance of enterococci as a nosocomial etiologic agent is well documented; however, enterococci are also capable of causing a variety of community-acquired infections. Vancomycin resistance in a clinical Enterococcus isolate was first reported in 1986, and since then vancomycin-resistant enterococci (VRE) have been reported world-wide. This report describes a case of E. faecium with the VanA phenotype, isolated from meningitis in Sao Paulo, Brazil. Two E. faecium strains were isolated. One strain showed VanA phenotype, and the molecular characterization of the VanA gene was confirmed by polymerase chain reaction. The other strain was susceptible to vancomycin and teicoplanin. The authors would like to call the attention of the scientific community to this first identification of a VRE case in Sao Paulo, Brazil.

Vancomycin resistance emerging in a clonal outbreak caused by ampicillin-resistant Enterococcus faecium

OBJECTIVES

To describe the first nosocomial outbreak of ampicillin-resistant Enterococcus faecium (ARE) in Norway, where a few vancomycin-resistant strains have also been identified.

METHODS

All cases of ARE and vancomycin-resistant Enterococcus faecium (VRE) diagnosed by the medical microbiological laboratories in a region inhabited by approximately 1 million people were registered. Isolates obtained during the period 1 January 1995 to 31 December 1996 were characterized by pulsed field-gel electrophoresis and the clinical data were recorded.

RESULTS

One hundred and forty-nine patients (64 males, 85 females, mean age 70.5 years) were infected with ARE. Isolates from 115 cases were genomically related to the outbreak strain. Infections included bacteremia (14), wound infections (31), urinary tract infections (97) and other infections (seven). Most had a severe underlying disease and 93% of the patients had received antibiotics for a mean time of 23 days. Twenty-four patients (16.1%) died during hospitalization. Four infections were caused by a vanB-type VRE that was genomically related to the ARE outbreak strain. The prescription rate for vancomycin was low, but an increase in vancomycin use paralleled the appearance of VRE. The highest monthly incidence rate was 2.5 per 1000 patient admissions in July 1996 declining to 0.5 in December 1996.

CONCLUSIONS

The first nosocomial outbreak caused by ARE was observed in 1995 in Norway and is still ongoing. One year after the onset, VRE occurred in wards which had a relatively high consumption of vancomycin.

Emergence of vancomycin-resistant enterococci in New York City

Enterococci, a common cause of nosocomial infection, are intrinsically resistant to most antimicrobials and readily acquire additional resistance. Vancomycin-resistant enterococci (VRE) have caused clusters of nosocomial infections since 1988. In April, 1991, the New York City Department of Health asked all city laboratories to submit suspected VRE isolates for confirmation. Clinical and epidemiological characteristics of the first 100 patients with VRE were identified, and antimicrobial susceptibility testing, restriction enzyme analysis, and DNA-DNA hybridisation with the vanA gene probe were done. From September, 1989, to October, 1991, 361 patients with VRE were identified at 38 hospitals. The number of hospitals reporting VRE increased from 1 in 1989 to 38 by October, 1991. 98% of 100 VRE infections were nosocomially acquired and 83% patients had received vancomycin and/or a cephalosporin in the 30 days before isolation of VRE. Of 23 isolates from 21 of the first 100 patients, 19 (83%) were resistant to all available antimicrobials. Four vanA probing patterns were noted, and restriction enzyme analysis of the 23 isolates revealed 14 strains. VRE have emerged rapidly in New York City. Molecular analyses suggest that a highly mobile genetic element--eg, a transposon--is responsible for the rapid spread of vancomycin resistance.

Frequency and antimicrobial susceptibility of clinical isolates of enterococci

A study was performed to determine the frequency and antimicrobial susceptibility of Enterococcus species in clinical specimens. Of 943 aesculin-positive isolates, 873 (92%) were identified as enterococci (737 Enterococcus faecalis, 129 Enterococcus faecium and 7 other Enterococcus species). High-level resistance to gentamicin was found in 15.2% of Enterococcus faecalis, but not in Enterococcus faecium; 58% of Enterococcus faecium were resistant to gentamicin at a concentration of 64 mg/l. None of the isolates were shown to possess vancomycin resistance.

The effect of selective decontamination of the digestive tract on gastrointestinal enterococcal colonization in ITU patients

OBJECTIVE

The effect of selective decontamination of the digestive tract (SDD) on Intensive Therapy Unit (ITU)-acquired enterococcal infection and colonization was studied. Changes in the predominant species isolated and resistance patterns to antimicrobial agents were also studied.

DESIGN

Three groups were investigated: historical control (HC), contemporaneous control (CC) and patients receiving SDD (topical polymyxin, amphotericin B and tobramycin throughout ITU stay with intravenous ceftazidime for the first 3 days only).

SETTING

Adult general ITU with 7 beds.

PATIENTS

Patients with a nasogastric tube in situ and who were likely to remain in ITU for 48 h or longer were recruited.

RESULTS

Enterococcal infections occurred in 3 of 84 HC patients and 2 of 91 CC patients. There were no unit-acquired enterococcal infections in the SDD group. There were 140 episodes of enterococcal colonization occurring in 112 patients, with significantly more in the SDD and CC groups (p < 0.05. There were no significant differences in antibiotic sensitivities between the three groups. Enterococcus faecalis was the most frequently isolated species.

CONCLUSION

SDD does not predispose to enterococcal infection but does encourage colonization in patients receiving the regimen and other patients in ITU at the same. There is a complex interaction of factors which influence faecal flora and the likelihood of patients becoming colonized or infected with enterococci.

Characterization of enterococcal isolates by restriction enzyme analysis of genomic DNA

A restriction enzyme analysis (REA) of chromosomal DNA for the intra-species characterization of enterococci is reported. The DNA was extracted by a rapid method and digested with the restriction enzyme Sal I to provide a characteristic 'fingerprint' consisting of 10-20 bands in the 1.6-5.0 kb range. One hundred and eighty enterococcal isolates were examined; 5 were type strains, 15 from an out-patient clinic and 160 from a geographically isolated British Antarctic Survey Base. The epidemiologically unrelated out-patient clinic isolates gave readily distinguishable patterns, whereas isolates from the geographically isolated community showed evidence of colonization. This technique provided a highly discriminatory method of isolate characterization for Enterococcus faecalis, E. faecium and E. durans suitable for epidemiological studies. A sample of isolates were probed with 16 + 23 S ribosomal RNA from Escherichia coli. Discrimination between isolates was poorer than with REA, although good correlation was observed between the results of the two techniques.

Antibiotic-resistant enterococci

Enterococci have emerged as an important cause of nosocomial infection. Successful antibiotic treatment of serious enterococcal infection usually depends on the synergistic bactericidal effect achieved by the combination of a cell wall-active agent, such as ampicillin or a glycopeptide, and an aminoglycoside. However, the prevalence of enterococci resistant to one or more of these antibiotics is increasing, and has resulted in serious therapeutic difficulties. The mechanisms of antibiotic resistance, and the epidemiology, laboratory diagnosis and management of infection with antibiotic-resistant enterococci are discussed.

Comparison of 30 microgram and 120 microgram gentamicin disks for the prediction of gentamicin resistance in Enterococcus faecalis

Single strain regression analysis was performed on PDM II medium for E. faecalis with 10, 30 and 120 micrograms gentamicin disks using E. faecalis, strain ATCC 29212 as the reference. This method permits the calculation of zone diameters corresponding to different MIC values for different disk contents. The lack of discrimination between normal low-level resistant strains and high-level resistance using the 10 micrograms disk was confirmed. However, both the 30 micrograms and 120 micrograms disks seemed to provide a separation of the normal low-level gentamicin-resistant population from strains with increased resistance. Since the 30 micrograms disk is used routinely in some countries, there should be no need for an extra high content disk in these laboratories. This was confirmed when 96 clinical isolates of E. faecalis were analysed and the results of routine disk diffusion tests were compared with the MIC values. Two of the strains showed high-level gentamicin resistance (greater than 2000 mg/l) and produced no zone of inhibition. The other 94 isolates showed gentamicin MIC values between 4-16 mg/l, and 72 of the MIC results were 8 mg/l. The zone diameters for these strains ranged between 15 and 25 mm with a mean of 18.2 and a median value of 18 mm. In order to include statistical considerations of the zone size populations for setting of breakpoints, a study of gentamicin zone size distributions was performed for several bacterial species. Inhibition zone diameter values around the 30 micrograms gentamicin disk for 2079 clinical isolates of E. faecalis, 2268 S. aureus, 3201 E. coli and 547 strains of P. mirabilis from different years were plotted as histograms. Tests for agreement with a Gaussian distribution showed that the histograms were slightly peaked and skewed towards higher zone values. Parametric and non-parametric statistical tests were compared and the results showed that means and medians were very similar and that parametric fractile estimations at the lower end of the histogram populations were conservative and could be used in view of a slightly lower rate of false resistance. The 1% parametric fractile of 12 mm was selected as a suitable breakpoint for the identification of normal, low-level resistant isolates of E. faecalis using the standardized disk test of the Swedish Reference Group for Antibiotics.

Synergistic killing of vancomycin-resistant enterococci of classes A, B, and C by combinations of vancomycin, penicillin, and gentamicin

Using both high and low inocula for time-kill curves, we examined the antibiotic killing of clinical isolates of glycopeptide-resistant enterococci (Enterococcus faecium, E. faecalis, and E. gallinarum) belonging to phenotypic resistance classes A, B, and C. None were resistant to high levels (greater than 500 mg/liter) of gentamicin. Vancomycin-penicillin-gentamicin resulted in 2 or more logs of killing above that of the most effective two-antibiotic combination for all strains except two of three E. gallinarum (VanC) strains and a constitutive mutant of a VanB strain. This strategy may be useful clinically.

Resistance to vancomycin and teicoplanin: an emerging clinical problem

Vancomycin and teicoplanin are glycopeptides active against a wide range of gram-positive bacteria. For 30 years following the discovery of vancomycin in 1956, vancomycin resistance was not detected among normally susceptible bacteria recovered from human specimens. Since 1986, however, bacteria resistant to vancomycin or teicoplanin or both have been described. Strains of the genera Leuconostoc, Lactobacillus, Pediococcus, and Erysipelothrix seem inherently resistant to glycopeptides. Species and strains of enterococci and coagulase-negative staphylococci appear to have acquired or developed resistance. There are at least two categories of glycopeptide resistance among enterococci, characterized by either high-level resistance to vancomycin (MIC, greater than or equal to 64 mg/liter) and teicoplanin (MIC, greater than or equal to 8 mg/liter) or lower-level vancomycin resistance (MIC, 32 to 64 mg/liter) and teicoplanin susceptibility (MIC, less than or equal to 1 mg/liter). The two categories appear to have similar resistance mechanisms, although genetic and biochemical studies indicate that they have arisen independently. Among coagulase-negative staphylococci, strains for which vancomycin MICs are up to 20 mg/liter or teicoplanin MICs are 16 to 32 mg/liter have been reported, but cross-resistance between these glycopeptides varies. The selective advantage accorded to glycopeptide-resistant bacteria and the observation that high-level resistance in enterococci is transferable suggest that such resistance may be expected to increase in incidence. Clinicians and microbiologists need to be aware of this emerging problem.