Pathogen Prevalence and Antimicrobial Susceptibility Among Enterobacteriaceae Causing Hospital-associated Intra-abdominal Infections in Adults in the United States (2012-2013)

Enterobacteriaceae predominate in the endophytic microbiome and contribute to the resistome of strawberry

Antibiotic resistance genes (ARGs) harbored by plant microbiomes have been implicated as a potential risk to public health via food chain, especially directly edible fruits and vegetables. Here, we investigated the microbiome and antibiotic resistome in soil-strawberry ecosystem using shotgun metagenomic sequencing. The results showed that the enterobacterial population dominated the endophytes of strawberry fruits. Moreover, 85 subtypes of ARGs, including several clinically important ARGs, were detected in the strawberry fruit metagenomes. Additionally, host tracking analysis in combination with antibiotic-resistant bacterial isolate screening suggested that fruit-borne ARGs were mainly carried by members of the Enterobacteriaceae family. Unexpectedly, most of fruit-borne isolates were found to be resistant to several clinically important antimicrobials, e.g., erythromycin and cephalexin. Our findings provide broad insights into endophytic antibiotic resistomes of direct edible strawberry fruits and their potential hosts, and highlight the potential exposure risks of plant microbiomes to the human food chain.

Optimizing therapy of bloodstream infection due to extended-spectrum β-lactamase-producing Enterobacteriaceae

PURPOSE OF REVIEW

Infections due to extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) are increasing worldwide. Carbapenems are usually regarded as the antibiotics of choice for the treatment of serious ESBL infections. However, because of the alarming emergence or carbapenem resistance, interest in effective alternatives has emerged. The present review summarizes the findings published on the antibiotics currently available for treatment of patients with an ESBL-E bloodstream infection (BSI).

RECENT FINDINGS

Meropenem and imipenem are the drugs recommended for treatment of ESBL BSIs in critically ill patients, and in infections with high bacterial loads or elevated β-lactam minimum inhibitory concentrations. Ertapenem should be reserved for patients with less severe presentations, and should be used at high doses. In milder presentations or BSIs from low-risk sources, other carbapenem-sparing alternatives could be considered: cephamycins, fluoroquinolones, and particularly a β-lactam/β-lactam inhibitor combination (particularly piperacillin/tazobactam). Optimized dosing of piperacillin/tazobactam is recommended (high doses and extended infusion). There are few data on the use of the promising newly available drugs (e.g. ceftolozane/tazobactam, ceftazidime/avibactam, cefiderocol, and plazomicin), and it seems reasonable to reserve them as last-resort drugs.

SUMMARY

Carbapenems should be used in patients with serious infections; alternatives could be used individually, particularly for definitive treatment of patients with milder presentations.

Evolution of antibiotic cross-resistance and collateral sensitivity in Staphylococcus epidermidis using the mutant prevention concentration and the mutant selection window

In bacteria, evolution of resistance to one antibiotic is frequently associated with increased resistance (cross-resistance) or increased susceptibility (collateral sensitivity) to other antibiotics. Cross-resistance and collateral sensitivity are typically evaluated at the minimum inhibitory concentration (MIC). However, these susceptibility changes are not well characterized with respect to the mutant prevention concentration (MPC), the antibiotic concentration that prevents a single-step mutation from occurring. We measured the MIC and the MPC for Staphylococcus epidermidis and 14 single-drug resistant strains against seven antibiotics. We found that the MIC and the MPC were positively correlated but that this correlation weakened if cross-resistance did not evolve. If any type of resistance did evolve, the range of concentrations between the MIC and the MPC tended to shift right and widen. Similar patterns of cross-resistance and collateral sensitivity were observed at the MIC and MPC levels, though more symmetry was observed at the MIC level. Whole-genome sequencing revealed mutations in both known-target and nontarget genes. Moving forward, examining both the MIC and the MPC may lead to better predictions of evolutionary trajectories in antibiotic-resistant bacteria.

In vitro activity of ceftolozane/tazobactam against phenotypically defined extended-spectrum β-lactamase (ESBL)-positive isolates of Escherichia coli and Klebsiella pneumoniae isolated from hospitalized patients (SMART 2016)

The Clinical and Laboratory Standards Institute (CLSI)-defined broth microdilution testing method (M07, 11th edition, 2018) was used to determine MICs for ceftolozane/tazobactam and eight comparator agents against 21,952 isolates of Enterobacteriaceae submitted by 161 clinical laboratories in 51 countries in 2016 as a part of the SMART global surveillance program. MICs were interpreted using CLSI breakpoints (M100 29th edition, 2019). 89.7% of isolates of Enterobacteriaceae were susceptible to ceftolozane/tazobactam, compared to 70.0%, 76.3%, 77.7%, 84.7%, 93.6%, and 96.4%, respectively, for ceftriaxone, ceftazidime, cefepime, piperacillin-tazobactam, ertapenem, and meropenem. 82.4% of isolates of ESBL-positive, carbapenemase-negative Enterobacteriaceae were susceptible to ceftolozane/tazobactam, compared to 1.5%, 7.8%, 20.3%, 71.1%, 94.7%, and 98.7%, respectively, for ceftriaxone, cefepime, ceftazidime, piperacillin-tazobactam, ertapenem, and meropenem. In vitro susceptibility to ceftolozane/tazobactam was >60% higher than susceptibility to other advanced-generation cephalosporins among all Enterobacteriaceae and >10% higher than susceptibility to piperacillin-tazobactam among ESBL-positive Enterobacteriaceae collected globally in 2016.

In vitro activity of imipenem/relebactam against Enterobacteriaceae and Pseudomonas aeruginosa isolated from intraabdominal and urinary tract infection samples: SMART Surveillance United States 2015-2017

OBJECTIVES

Antimicrobial resistance, including multidrug-resistance (MDR), is increasing, especially among Gram-negative bacilli. New agents are needed to treat infections caused by these pathogens. This report assessed the activity of imipenem/relebactam against Gram-negative bacilli from intraabdominal infections (IAIs) and urinary tract infections (UTIs) submitted to the SMART (Study for Monitoring Antimicrobial Resistance Trends) global surveillance programme in the United States from 2015 to 2017.

METHODS

Broth microdilution MICs for imipenem/relebactam and comparators were determined by a central laboratory against isolates of non-Proteeae Enterobacteriaceae (NPE) and Pseudomonas aeruginosa (P. aeruginosa). Imipenem/relebactam MICs were interpreted using United States Food and Drug Administration (FDA) breakpoints.

RESULTS

99.5% of NPE isolates collected from patients with IAIs (n=3633) and UTIs (n=3038) were susceptible to imipenem/relebactam, as were 77.9% of imipenem-nonsusceptible, 96.3% of Klebsiella pneumoniae carbapenemase (KPC)-positive, and 98.7% of MDR isolates from IAIs and UTIs combined. A total of 96.7% of IAI isolates (n=486) and 96.4% of UTI isolates (n=360) of P. aeruginosa were susceptible to imipenem/relebactam, as were 85.0% of imipenem-nonsusceptible and 87.3% of MDR isolates from IAIs and UTIs combined. Percent susceptibility to imipenem/relebactam for cefepime-, ceftazidime-, and piperacillin-tazobactam-nonsusceptible isolates was 98.3-98.8% for NPE and 87.3-90.0% for P. aeruginosa.

CONCLUSIONS

Imipenem/relebactam demonstrated potent in vitro activity against NPE and P. aeruginosa isolates from IAIs and UTIs, including against resistant subsets, and will provide important coverage for IAIs and UTIs caused by β-lactam-resistant, MDR, and KPC-positive Gram-negative bacilli.

Critically ill patients with community-onset intraabdominal infections: Influence of healthcare exposure on resistance rates and mortality

The concept of healthcare-associated infections (as opposed to hospital-acquired infections) in intraabdominal infections (IAIs) is scarcely supported by data in the literature. The aim of the present study was to analyse community-onset IAIs (non-postoperative/non-nosocomial) in patients admitted to intensive care units (ICUs), to investigate differences in resistance patterns linked to healthcare exposure and mortality-associated factors. A one-year prospective observational study (17 Spanish ICUs) was performed distributing cases as healthcare-associated infections (HCAI), community-acquired infections (CAI) and immunocompromised patients (ICP). Bacteria producing extended-spectrum β-lactamases (ESBL) and/or carbapenemase (CPE), high-level aminoglycoside- and/or methicillin- and/or vancomycin- resistance were considered antimicrobial resistant (AMR). Mortality-associated factors were identified by regression multivariate analysis. Of 345 patients included (18.8% HCAI, 6.1% ICP, 75.1% CAI), 51.6% presented generalized peritonitis; 32.5% were >75 years (55.4% among HCAI). Overall, 11.0% cases presented AMR (7.0% ESBL- and/or CPE), being significantly higher in HCAI (35.4%) vs. CAI (5.8%) (p<0.001) vs. ICP (0%) (p = 0.003). Overall 30-day mortality was 14.5%: 23.1% for HCAI and 11.6% for CAI (p = 0.016). Mortality (R2 = 0.262, p = 0.021) was positively associated with age >75 years (OR = 6.67, 95%CI = 2.56-17.36,p<0.001), Candida isolation (OR = 3.05, 95%CI = 1.18-7.87,p = 0.022), and SAPS II (per-point, OR = 1.08, 95%CI = 1.05-1.11, p<0.001) and negatively with biliary infections (OR = 0.06, 95%CI = 0.01-0.48,p = 0.008). In this study, the antimicrobial susceptibility pattern of bacteria isolated from patients with healthcare contact was shifted to resistance, suggesting the need for consideration of the healthcare category (not including hospital-acquired infections) for severe IAIs. 30-day mortality was positively related with age >75 years, severity and Candida isolation but not with AMR.

Trends in resistant Enterobacteriaceae and Acinetobacter species in hospitalized patients in the United States: 2013-2017

BACKGROUND

Trends in antimicrobial resistance help inform infection control efforts. We examined trends in resistance for Enterobacteriaceae and Acinetobacter spp. from 2013 to 2017 in hospitalized US patients.

METHODS

We analyzed antimicrobial susceptibility of non-duplicate isolates in hospitalized patients (not limited to hospital-acquired infections) in the US BD Insights Research Database. Resistance profiles of interest were extended-spectrum beta-lactamase (ESBL)-producing, multidrug resistant (MDR), and carbapenem-nonsusceptible (Carb-NS) phenotypes of Enterobacteriaceae, and MDR and Carb-NS Acinetobacter spp. Time series models were used to evaluate the patterns of resistance trends in rate per 100 hospital admissions and proportion per isolates tested.

RESULTS

More than 1 million Enterobacteriaceae isolates were obtained from 411 hospitals; 12.05% were ESBL, 1.21% Carb-NS, and 7.08% MDR. Urine was the most common source. For Acinetobacter spp. (n = 19,325), 37.48% were Carb-NS, 47.66% were MDR, and the most common source was skin/wound cultures. Trend analyses showed that the rates of ESBL and Carb-NS Enterobacteriaceae per 100 hospital admissions increased significantly between 2013 and 2017. Rates of MDR Enterobacteriaceae and Carb-NS and MDR Acinetobacter spp. decreased during this time period. Trends in proportions of resistant isolates generally mirrored trends in rates per 100 hospital admissions. MDR Enterobacteriaceae and Carb-NS and MDR Acinetobacter spp. were more common in winter than summer.

CONCLUSIONS

In this large-scale study of patients in US hospitals, rates of ESBL and Carb-NS Enterobacteriaceae per 100 hospital admissions increased between 2013 and 2017. MDR Enterobacteriaceae and MDR and Carb-NS Acinetobacter spp. isolates decreased over this period. These data support continuing infection control and stewardship efforts and the development of new therapeutic options.

Activity of ceftolozane-tazobactam and comparators against Pseudomonas aeruginosa from patients in different risk strata - SMART United States 2016-2017

OBJECTIVES

Infections caused by Pseudomonas aeruginosa are often difficult to treat. Knowledge of the risk of infection with resistant P. aeruginosa would allow more discriminatory prescribing of broad-spectrum antimicrobials. Using clinical isolates collected as part of the Study for Monitoring Antimicrobial Resistance Trends (SMART), we examined the activity of commonly used β-lactams, levofloxacin, and ceftolozane-tazobactam (C/T), an antipseudomonal cephalosporin/β-lactamase inhibitor approved in the United States and over 60 countries worldwide, against P. aeruginosa isolates from patients in different risk strata.

METHODS

In 2016-2017, 25 hospitals in the US each collected up to 250 consecutive gram-negative bacilli per year from respiratory tract (RTI), intraabdominal (IAI), and urinary tract (UTI) infections. MICs of 9,964 isolates (including 1,887 P. aeruginosa) were determined using CLSI broth microdilution and interpreted with CLSI breakpoints.

RESULTS

Susceptibility of all P. aeruginosa isolates combined was 94.7% to C/T and 76.8%, 77.0%, 70.2%, and 69.0% to ceftazidime, meropenem, piperacillin-tazobactam, and levofloxacin, respectively. Susceptibility to the β-lactam comparators was 8-11 percentage points lower among ICU than non-ICU isolates, 7-11 points lower in isolates collected ≥48h than <48h post-admission, 1-5 points lower in patients <65 years of age than older patients, and 3-12 points lower in RTI than IAI and UTI isolates. C/T maintained activity against >90% of P. aeruginosa isolates in all risk strata and against 75-88% of isolates nonsusceptible to ceftazidime, meropenem, or piperacillin-tazobactam.

CONCLUSIONS

C/T represents a promising new treatment option even in strata in which the risk of infection with β-lactam-nonsusceptible P. aeruginosa appeared higher.

Current options for the treatment of infections due to extended-spectrum beta-lactamase-producing Enterobacteriaceae in different groups of patients

BACKGROUND

Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) are a frequent cause of invasive infections worldwide. Carbapenems are nowadays the most used drugs to treat these infections. However, due to the increasing rates of resistance to these antimicrobials, carbapenem-sparing alternatives are being investigated.

OBJECTIVES AND SOURCES

The aim of this narrative literature review is to summarize the published information on the currently available antibiotics for the treatment of ESBL-E infections, providing specific information on three subgroups of patients: Group 1, patients with severe infections or infections from high-risk sources or in severely immunocompromised patients; Group 2, patients with non-severe infections from intermediate-risk source; and Group 3, patients with non-severe urinary tract infection.

CONTENT AND IMPLICATIONS

For patients in Group 1, the current data would support the use of carbapenems. For milder infections, however, particularly urinary tract infections, other non-carbapenem antibiotics can be considered in selected cases, including beta-lactam/beta-lactam inhibitor combinations, cephamycins, temocillin and aminoglycosides. While specific studies should be performed in these situations, individualized decisions may be taken in order to avoid overuse of carbapenems.

Fluoroquinolone-based versus β-lactam-based regimens for complicated intra-abdominal infections: a meta-analysis of randomised controlled trials

Complicated intra-abdominal infections (cIAIs) are common and confer significant morbidity, mortality and costs. In this era of evolving antimicrobial resistance, selection of appropriate empirical antimicrobials is paramount. This systematic review and meta-analysis of randomised controlled trials compared the effectiveness and safety of fluoroquinolone (FQ)-based versus β-lactam (BL)-based regimens for the treatment of patients with cIAIs. Primary outcomes were treatment success in the clinically evaluable (CE) population and all-cause mortality in the intention-to-treat (ITT) population. Subgroup analyses were performed based on specific antimicrobials, infection source and isolated pathogens. Seven trials (4125 patients) were included. FQ-based regimens included moxifloxacin (four studies) or ciprofloxacin/metronidazole (three studies); BL-based regimens were ceftriaxone/metronidazole (three studies), carbapenems (two studies) or piperacillin/tazobactam (two studies). There was no difference in effectiveness in the CE (2883 patients; RR = 1.00, 95% CI 0.95-1.04) or ITT populations (3055 patients; RR = 0.97, 95% CI 0.94-1.01). Mortality (3614 patients; RR = 1.04, 95% CI 0.75-1.43) and treatment-related adverse events (2801 patients; RR = 0.97, 95% CI 0.70-1.33) were also similar. On subset analysis, moxifloxacin was slightly less effective than BLs in the CE (1934 patients; RR = 0.96, 95% CI 0.93-0.99) and ITT populations (1743 patients; RR = 0.94, 95% CI 0.91-0.98). Although FQ- and BL-based regimens appear equally effective and safe for the treatment of cIAIs, limited data suggest slightly inferior results with moxifloxacin. Selection of empirical coverage should be based on local bacterial epidemiology and patterns of resistance as well as antimicrobial stewardship protocols.

Shifting trends in bacteriology and antimicrobial resistance among gastrointestinal fistula patients in China: an eight-year review in a tertiary-care hospital

Background

The purpose of this study was to determine the shifting trends in bacteriology and antimicrobial resistance of infectious specimens isolated from gastrointestinal (GI) fistula patients over eight years in China.

Methods

We retrospectively reviewed the microbial records of intra-abdominal specimens at a teaching hospital from 2008 to 2015. Study period was divided into the first half (2008–2011) and the second half (2012–2015). All isolates underwent antibiotic susceptibility testing by the micro dilution method.

Results

A total of 874 intra-abdominal isolates were consecutively collected from 502 GI fistula patients (mean age, 46.5 years, 71.1% male) during the study period. Patients in the second study period (2012–2015) were older (>65 years) and more likely to have experienced cancer. Over the entire study period, most infections were caused by E. coli (24.2%) and K. pneumonia (14.1%). There was a significant decrease in the proportion E. coli isolates that were extended- spectrum beta-lactamase (ESBL)-positive (P = 0.026). The proportion of E. coli resistant to imipenem increased from 14.3% in 2008–2011 to 25.9% in 2012–2015 (P = 0.037). Imipenem resistance prevalence was higher in ESBL-negative bacteria than ESBL-positive bacteria for both E. coli and K. pneumonia (P < 0.001). In Enterococcus, significant increase in resistance to ampicillin (P = 0.01) and moxifloxacin (P = 0.02) over time were observed. In Staphylococcus and fungi, rates of antibiotic resistance did not significantly change over the study period.

Conclusions

Gram-negative bacteria predominated as causative agents of intra-abdominal infections in GI fistula patients, and there was an increase in levels of resistance to certain antibiotics, particularly carbapenems. Infection control and source control are important tools available to surgeons to prevent the emergence of antibiotic-resistant pathogens.

Electronic supplementary material

The online version of this article (10.1186/s12879-017-2744-7) contains supplementary material, which is available to authorized users.

Management of intra-abdominal infections: recommendations by the WSES 2016 consensus conference

This paper reports on the consensus conference on the management of intra-abdominal infections (IAIs) which was held on July 23, 2016, in Dublin, Ireland, as a part of the annual World Society of Emergency Surgery (WSES) meeting. This document covers all aspects of the management of IAIs. The Grading of Recommendations Assessment, Development and Evaluation recommendation is used, and this document represents the executive summary of the consensus conference findings.

Ceftolozane/tazobactam and ceftazidime/avibactam for the treatment of complicated intra-abdominal infections

Complicated intra-abdominal infections (cIAI) represent a large proportion of all hospital admissions and are a major cause of morbidity and mortality in the intensive care unit. Rising rates of multidrug resistant organisms (MDRO), including extended-spectrum β-lactamase producing Enterobacteriaceae and carbapenem-nonsusceptible Pseudomonas spp., for which there are few remaining active antimicrobial agents, pose an increased challenge to clinicians. Patients with frequent exposures to the health care system or multiple recurrent IAIs are at increased risk for MDRO; however, treatment options have traditionally been limited, in some cases necessitating the utilization of last-line agents with unfavorable side-effect profiles. Ceftolozane/tazobactam and ceftazidime/avibactam are two new cephalosporin and β-lactamase inhibitor combinations with recent US Food and Drug Administration approvals for the treatment of cIAI in combination with metronidazole. Ceftolozane/tazobactam has demonstrated excellent in vitro activity against MDR and extensively drug-resistant Pseudomonas spp., including carbapenem-nonsusceptible strains, while ceftazidime/avibactam effectively inhibits a broad range of β-lactamases, making it an excellent option for the treatment of carbapenem-resistant Enterobacteriaceae. Both agents were shown to be noninferior to meropenem for treatment of cIAI in Phase III trials; however, reduced responses in patients with renal impairment at baseline highlight the importance of routine serum creatinine monitoring and ongoing dose adjustments. This review highlights in vitro and in vivo data of these two agents and suggests their proper place in cIAI treatment to ensure adequate therapy in our most at-risk patients while sparing unnecessary use in patients without MDRO risk factors.

In vitro potency of amikacin and comparators against E. coli, K. pneumoniae and P. aeruginosa respiratory and blood isolates

Background

The purpose of this study was to define the potency of amikacin and comparator agents against a collection of blood and respiratory nosocomial isolates implicated in ICU based pulmonary infections gathered from US hospitals.

Methods

Minimum inhibitory concentrations of amikacin, aztreonam, cefepime, ceftazidime, ceftolozane/tazobactam, ceftriaxone, ciprofloxacin, imipenem, meropenem, piperacillin/tazobactam and tobramycin were tested against 2460 Gram-negative isolates. Amikacin had 96 % susceptibility against the combined E. coli and K. pneumoniae isolates and 95 % susceptibility against P. aeruginosa.

Results

Ninety-six percent of all of isolates tested were susceptible (i.e., MICs ≤16 mg/L) to amikacin by current laboratory standards which demonstrates a high level of activity to combat infections caused by these organisms including ESBL, MDR, β-lactam and fluoroquinolone resistant strains. Moreover, 99 % of all organisms had amikacin MICs ≤64 mg/L.

Conclusions

Overall, these data highlight the continued potency of amikacin and suggest that the achievable lung concentrations of approximately 5000 mg/L with the administration of the amikacin by inhalation (Amikacin Inhale, BAY41-6551) will exceed the MICs typically observed for P. aeruginosa, E. coli and K. pneumoniae in the hospital setting.