Community-associated extended-spectrum β-lactamase-producing Escherichia coli infection in the United States

Definition and diagnosis of fracture-related infection

Fracture-related infection (FRI) is common and often diagnosed late.Accurate diagnosis is the beginning of effective treatment.Diagnosis can be difficult, particularly when there are no outward signs of infection.The new FRI definition, together with clear protocols for nuclear imaging, microbiological culture and histological analysis, should allow much better study design and a clearer understanding of infected fractures.In recent years, there has been a new focus on defining FRI and avoiding non-specific, poorly targeted treatment. Previous studies on FRI have often failed to define infection precisely and so are of limited value. This review highlights the essential principles of making the diagnosis and how clinical signs, serum tests, imaging, microbiology, molecular biology and histology all contribute to the diagnostic pathway. Cite this article: EFORT Open Rev 2020;5:614-619. DOI: 10.1302/2058-5241.5.190072.

Multidrug-Resistant Bacteria in the Community: An Update

Multidrug-resistant bacteria are among the most important current threats to public health. Typically, they are associated with nosocomial infections. However, some have become prevalent causes of community-acquired infections, such as Neisseria gonorrhoeae, Shigella, Salmonella, and Streptococcus pneumoniae. The community spread of multidrug-resistant bacteria is also a crucial development. An important global threat on the horizon is represented by production of carbapenemases by community-acquired hypervirulent Klebsiella pneumoniae. Such strains have already been found in Asia, Europe, and North America. Prevention of further community spread of multidrug-resistant bacteria is of the utmost importance, and will require a multidisciplinary approach involving all stakeholders.

The Continuing Plague of Extended-Spectrum β-Lactamase Producing Enterbacterales Infections: An Update

Antimicrobial resistance is a common iatrogenic complication of modern life and medical care. One of the most demonstrative examples is the exponential increase in the incidence of extended-spectrum β-lactamases (ESBLs) production among Enterobacteriaceae, that is, the most common human pathogens outside of the hospital setting. Infections resulting from ESBL-producing bacteria are associated with devastating outcomes, now affecting even previously healthy individuals. This poses an enormous burden and threat to public health. This article aims to narrate the evolving epidemiology of ESBL infections and highlights current challenges in terms of management and prevention of these common infections.

Does the presence of multiple β-lactamases in Gram-negative bacilli impact the results of antimicrobial susceptibility tests and extended-spectrum β-lactamase and carbapenemase confirmation methods?

OBJECTIVES

Many multidrug-resistant Gram-negative bacilli (MDR-GNB) harbour multiple β-lactamases. The aim of this study was to assess the impact of multiple β-lactamase carriage on the accuracy of susceptibility tests and extended-spectrum β-lactamase (ESBL) and carbapenemase confirmation methods.

METHODS

A total of 50 MDR-GNB, of which 29 carried multiple β-lactamases, underwent broth microdilution (BMD) and disk diffusion (DD) testing as well as confirmation tests for ESBLs and carbapenemases. Whole-genome sequencing (WGS) was used for β-lactamase gene identification.

RESULTS

Categorical agreement of BMD and DD testing results ranged from 86.5 to 97.7% for 10 β-lactam agents. BMD and DD algorithms for ESBL detection were highly variable; 6 of 8 positive strains carried an ESBL plus a carbapenemase or an AmpC enzyme, which may confound antimicrobial selection. The sensitivity and specificity of the modified carbapenem inactivation method (mCIM) were both 100%, whilst mCIM and EDTA-modified carbapenem inactivation method (eCIM) when used together to differentiate serine from metallo-β-lactamase carriage were both 96%. Xpert® Carba-R results (in vitro diagnostic test) were consistent with WGS results. Predicting phenotypic carbapenem resistance from WGS data overall showed 100% specificity but only 66.7% sensitivity for Enterobacterales isolates that were non-susceptible to imipenem and meropenem.

CONCLUSIONS

Multiple β-lactamases in MDR-GNB does not impact DD results, the utility of mCIM/eCIM tests, or Xpert Carba-R results. However, ESBL algorithms produced inconsistent results and predicting carbapenem resistance from WGS data was problematic in such strains.

A Dual Enzyme-Based Biochemical Test Rapidly Detects Third-Generation Cephalosporin-Resistant CTX-M-Producing Uropathogens in Clinical Urine Samples

Extended-spectrum β-lactamase (ESBL)-producing Gram-negative bacteria (GNB) are increasingly identified as the cause of both community and healthcare-associated urinary tract infections (UTIs), with CTX-Ms being the most common ESBLs identified. CTX-M-producing GNB are resistant to most β-lactam antibiotics and are frequently multidrug-resistant, which limits treatment options. Rapid diagnostic tests that can detect ESBL-producing GNB, particularly CTX-M producers, in the urine of patients with UTIs are needed. Results from such a test could direct the selection of appropriate antimicrobial therapy at the point-of-care (POC). In this study, we show that a chromogenic, dual enzyme-mediated amplification system (termed DETECT [dual-enzyme trigger-enabled cascade technology]) can identify CTX-M-producing GNB from unprocessed urine samples in 30 minutes. We first tested DETECT against a diverse set of recombinant β-lactamases and β-lactamase-producing clinical isolates to elucidate its selectivity. We then tested DETECT with 472 prospectively collected clinical urine samples submitted for urine culture to a hospital clinical microbiology laboratory. Of these, 118 (25%) were consistent with UTI, 13 (11%) of which contained ESBL-producing GNB. We compared DETECT results in urine against a standard phenotypic method to detect ESBLs, and polymerase chain reaction and sequencing for CTX-M genes. DETECT demonstrated 90.9% sensitivity and 97.6% specificity (AUC, 0.937; 95% confidence interval, 0.822-1.000), correctly identifying 10 of 11 urine samples containing a clinically significant concentration of CTX-M-producing GNB (including Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis). Our results demonstrate the clinical potential of DETECT to deliver diagnostic information at the POC, which could improve initial antibiotic selection.

Genomic Surveillance of Ceftriaxone-Resistant Escherichia coli in Western New York Suggests the Extended-Spectrum β-Lactamase bla CTX-M-27 Is Emerging on Distinct Plasmids in ST38

Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae pose significant treatment and infection prevention challenges. Escherichia coli sequence type (ST) 131 associated with the bla_CTX-M-15 gene has been the dominant lineage of ESBL-producing E. coli in the US and worldwide. In this study, our objective was to determine the β-lactamase profile, means of dissemination, prevalence, and the clonal identity of ESBL-producing E. coli in our region of Western New York. Whole-genome SNP-based phylogenomics was used to assess 89 ceftriaxone-resistant (CTR) E. coli. Isolates were collected from both inpatients and outpatients and from urine and sterile-sites over a 2 month period in 2017 or throughout the year, respectively. ST131 was the predominant ST (46.0%), followed by ST38 (15.7%). The bla_CTX-M-15 gene was commonly found in 53.7% of ST131 isolates, whereas the bla_CTX-M-27 gene was found in 26.8% of ST131, though was significantly associated with ST38, and was found in 71.4% of those strains. When compared to ST131, ST38 E. coli exhibited increased frequency of resistance to nitrofurantoin and decreased frequency of resistance to ciprofloxacin and ampicillin-sulbactam. Using Nanopore long-read sequencing technology, an analysis of the ESBL genetic context showed that the bla_CTX-M-15 gene was chromosomal in 68.2% of ST131, whereas the bla_CTX-M-27 gene was plasmid-borne in all ST131 and 90% of ST38 isolates. Notably, the bla_CTX-M-27 gene in ST38 resided on highly-related (99.0–100.0% identity and 65.0–98.0% query coverage) conjugative IncF plasmids of distinct plasmid multi-locus sequence types (pMLSTs) from those in ST131. Furthermore, ST131 and ST38 were found to harbor different antibiotic resistance gene and virulence factor profiles. These findings raise the possibility of an emerging ESBL-producing E. coli lineage in our region.

Characteristics of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae and Contact to Animals in Estonia

We have attempted to define the prevalence and risk factors of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-Enterobacteriaceae) carriage, and to characterize antimicrobial susceptibility, beta-lactamase genes, and major types of isolated strains in volunteers, with a specific focus on humans in contact with animals. Samples were collected from 207 volunteers (veterinarians, pig farmers, dog owners, etc.) and cultured on selective agar. Clonal relationships of the isolated ESBL-Enterobacteriaceae were determined by whole genome sequencing and multi-locus sequence typing. Beta-lactamases were detected using a homology search. Subjects filled in questionnaires analyzed by univariate and multiple logistic regression. Colonization with ESBL-Enterobacteriaceae was found in fecal samples of 14 individuals (6.8%; 95%CI: 3.75–11.09%). In multiple regression analysis, working as a pig farmer was a significant risk factor for ESBL-Enterobacteriaceae carriage (OR 4.8; 95%CI 1.2–19.1). The only species isolated was Escherichia coli that distributed into 11 sequence types. All ESBL-Enterobacteriaceae isolates were of CTX-M genotype, with the blaCTX-M-1 being the most prevalent and more common in pig farmers than in other groups. Despite the generally low prevalence of ESBL-Enterobacteriaceae in Estonia, the pig farmers may still pose a threat to transfer resistant microorganisms. The clinical relevance of predominant blaCTX-M-1 carrying E. coli is still unclear and needs further studies.

Does inappropriate initial antibiotic therapy affect in-hospital mortality of patients in the emergency department with Escherichia coli and Klebsiella pneumoniae bloodstream infections?

Extended-spectrum β-lactamase (ESBL)-positive bloodstream infection (BSI) is on the rise worldwide. The purpose of this study is to evaluate the impact of inappropriate initial antibiotic therapy (IIAT) on in-hospital mortality of patients in the emergency department (ED) with Escherichia coli and Klebsiella pneumoniae BSIs. This retrospective single-center cohort study included all adult patients with E. coli and K. pneumoniae BSIs between January 2007 and December 2013, who had undergone a blood culture test and initiation of antibiotics within 6 h of ED registration time. Multiple logistic regression was used to adjust for bacterial species, IIAT, time to antibiotics, age, sex, quick Sepsis Related Organ Failure Assessment (qSOFA) score ⩾ 2, and comorbidities. A total of 3533 patients were enrolled (2967 alive and 566 deceased, in-hospital mortality rate 16%). The patients with K. pneumoniae ESBL-positive BSI had the highest mortality rate. Non-survivors had qSOFA scores ⩾ 2 (33.6% vs 9.5%, P < 0.001), more IIAT (15.0% vs 10.7%, P = 0.004), but shorter mean time to antibiotics (1.70 vs 1.84 h, P < 0.001). A qSOFA score ⩾ 2 is the most significant predictor for in-hospital mortality; however, IIAT and time to antibiotics were not significant predictors in multiple logistic regression analysis. In subgroup analysis divided by qSOFA scores, IIAT was still not a significant predictor. Severity of the disease (qSOFA score ⩾ 2) is the key factor influencing in-hospital mortality of patients with E. coli and K. pneumoniae BSIs. The time to antibiotics and IIAT were not significant predictors because they in turn were affected by disease severity.

Carriage of Extended-spectrum Beta-lactamase-producing Enterobacteriaceae and the Risk of Surgical Site Infection After Colorectal Surgery: A Prospective Cohort Study

BACKGROUND

Antibiotic prophylaxis that covers enteric pathogens is essential in preventing surgical site infections (SSIs) after colorectal surgery. Current prophylaxis regimens do not cover extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE). We aimed to determine whether the risk of SSI following colorectal surgery is higher in ESBL-PE carriers than in noncarriers.

METHODS

We conducted a prospective cohort study of patients who underwent elective colorectal surgery in 3 hospitals in Israel, Switzerland, and Serbia between 2012 and 2017. We included patients who were aged ≥18 years, were screened for ESBL-PE carriage before surgery, received routine prophylaxis with a cephalosporin plus metronidazole, and did not have an infection at the time of surgery. The exposed group was composed of ESBL-PE-positive patients. The unexposed group was a random sample of ESBL-PE-negative patients. We collected data on patient and surgery characteristics and SSI outcomes. We fit logistic mixed effects models with study site as a random effect.

RESULTS

A total of 3600 patients were screened for ESBL-PE; 13.8% were carriers SSIs occurred in 55/220 carriers (24.8%) and 49/440 noncarriers (11.1%, P < .001). In multivariable analysis, ESBL-PE carriage more than doubled the risk of SSI (odds ratio [OR], 2.36; 95% confidence interval [CI], 1.50-3.71). Carriers had higher risk of deep SSI (OR, 2.25; 95% CI, 1.27-3.99). SSI caused by ESBL-PE occurred in 7.2% of carriers and 1.6% of noncarriers (OR, 4.23; 95% CI, 1.70-10.56).

CONCLUSIONS

ESBL-PE carriers who receive cephalosporin-based prophylaxis are at increased risk of SSI following colorectal surgery.

Clinical and Molecular Epidemiology of Extended-Spectrum Beta-Lactamase-Producing Escherichia Coli Infections in Metro Detroit: Early Dominance of the ST-131 Clone

INTRODUCTION

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli infections have become endemic worldwide. We aimed to describe the molecular and clinical epidemiology of ESBL-producing E. coli infections during a period of rising global prevalence.

METHODS

Three hundred sixty-nine consecutive ESBL-producing E. coli infections in Detroit from 2010-2011 were analyzed. Sequence typing (ST) and CH typing were performed. Clinical characteristics and outcomes were compared between patients infected with ST131 and non-ST131 isolates.

RESULTS

Ninety-six percent of isolates were ST 131, and 78.6% of ST 131 isolates produced bla_CTX-M-15. Median time to effective therapy was 48 h vs. 35 h (P = 0.38) in the ST131 vs. non-ST131 groups. Ninety-day mortality rates (8% vs. 8%, P = 1.0) were similar between the two groups.

CONCLUSION

bla_CTX-M-15 ST131 E. coli predominated in Detroit during an early period of global ST131 dissemination. Patients with ST131 E. coli infections had similar clinical outcomes to those with non-ST131 E. coli infections.

Molecular Mechanisms, Epidemiology, and Clinical Importance of β-Lactam Resistance in Enterobacteriaceae

Despite being members of gut microbiota, Enterobacteriaceae are associated with many severe infections such as bloodstream infections. The β-lactam drugs have been the cornerstone of antibiotic therapy for such infections. However, the overuse of these antibiotics has contributed to select β-lactam-resistant Enterobacteriaceae isolates, so that β-lactam resistance is nowadays a major concern worldwide. The production of enzymes that inactivate β-lactams, mainly extended-spectrum β-lactamases and carbapenemases, can confer multidrug resistance patterns that seriously compromise therapeutic options. Further, β-lactam resistance may result in increases in the drug toxicity, mortality, and healthcare costs associated with Enterobacteriaceae infections. Here, we summarize the updated evidence about the molecular mechanisms and epidemiology of β-lactamase-mediated β-lactam resistance in Enterobacteriaceae, and their potential impact on clinical outcomes of β-lactam-resistant Enterobacteriaceae infections.

Differential Trends in Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Infections in Four Health Care Facilities in a Single Metropolitan Area: A Retrospective Analysis

Background: Prevalence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli) is increasing worldwide, but greatly varies geographically. We compared the prevalence of ESBL-E. coli infections at four distinct health care facilities in San Francisco, California. Methods: Antimicrobial susceptibility reports were obtained for E. coli isolates from (1) a county hospital, (2) a public skilled nursing facility, (3) a university hospital, and (4) a Veterans Affairs (VA) Medical Center. We compared change in frequency of ESBL-E. coli and antimicrobial resistance to trimethoprim-sulfamethoxazole between 2012 and 2018. Results: From 2012 to 2018, frequency of ESBL-E. coli increased in urine and nonurine isolates from the county hospital (urine: 1.1% per year, 95% confidence interval [CI]: 0.5-1.6, p < 0.01; nonurine: 1.9% per year, 95% CI: 0.9-2.9, p < 0.01) and in urine isolates from the VA hospital (0.9% per year, 95% CI: 0.3-1.4, p < 0.01). The frequency of trimethoprim-sulfamethoxazole resistance fluctuated in all facilities. Conclusions: At the skilled nursing facility, the prevalence of ESBL-E. coli was highest, but remained stable over time, while the prevalence of ESBL-E. coli increased among urine and nonurine isolates at the county hospital and urine isolates at the VA hospital. The temporal trend of ESBL-E. coli infections, even within one city, varied by health care facility.

The Clinical Significance of High Antimicrobial Resistance in Community-Acquired Urinary Tract Infections

Background

Urinary tract infections (UTIs) affect up to 150 million individuals annually worldwide, mainly due to Escherichia coli (E. coli) and Klebsiella. The emergence and spread of multidrug-resistant (MDR) bacteria are increasing, representing one of the biggest threats for human health. The objective of our study was to describe antimicrobial patterns of resistance and identify risk factors associated with MDR uropathogens.

Methods

We conducted a cross-sectional study in 296 patients with community-acquired UTI who underwent clinical and microbiologic analysis, and clinical associations to MDR uropathogens were investigated. Findings. Microbiological analysis included E. coli (55%), ESBL-E. coli (26%), Enterococcus (6%), Klebsiella (5%), and others (8%). Higher frequencies of MDR bacteria were found among ESBL-E. coli, with resistance to ampicillin (100%), ceftriaxone (96%), gentamicin (57%), ciprofloxacin (89%), and TMP/SMX (53%). However, they were sensitive to fosfomycin (6.6%), nitrofurantoin (1.3%), and carbapenems (0%). Fosfomycin MIC90 for ESBL-E. coli was 5.78 μg/mL. The only clinical variable with significant association to ESBL producers was the presence of comorbidities: hypertension and type 2 diabetes mellitus with an OR (95%CI) of 2.5(1.3 − 4.9)(p < 0.01) and 2.8(1.2 − 6.7)(p < 0.05), respectively.

Conclusions

In the majority of cases, resistance rates to commonly prescribed antimicrobials in UTIs were high, except for fosfomycin, nitrofurantoin, and carbapenems. To provide appropriate treatment, both the identification of risk factors and the uropathogen would be important. An active surveillance in UTIs in the community is required since the proportion of ESBL producers is increasing.

A prospective study of bloodstream infections among febrile adolescents and adults attending Yangon General Hospital, Yangon, Myanmar

Data on causes of community-onset bloodstream infection in Myanmar are scarce. We aimed to identify etiological agents of bloodstream infections and patterns of antimicrobial resistance among febrile adolescents and adults attending Yangon General Hospital (YGH), Yangon, Myanmar. We recruited patients ≥12 years old with fever ≥38°C who attended YGH from 5 October 2015 through 4 October 2016. A standardized clinical history and physical examination was performed. Provisional diagnoses and vital status at discharge was recorded. Blood was collected for culture, bloodstream isolates were identified, and antimicrobial susceptibility testing was performed. Using whole-genome sequencing, we identified antimicrobial resistance mechanisms of Enterobacteriaceae and sequence types of Enterobacteriaceae and Streptococcus agalactiae. Among 947 participants, 90 (9.5%) had bloodstream infections (BSI) of which 82 (91.1%) were of community-onset. Of 91 pathogens isolated from 90 positive blood cultures, we identified 43 (47.3%) Salmonella enterica including 33 (76.7%) serovar Typhi and 10 (23.3%) serovar Paratyphi A; 20 (22.0%) Escherichia coli; 7 (7.7%) Klebsiella pneumoniae; 6 (6.6%), Staphylococcus aureus; 4 (4.4%) yeasts; and 1 (1.1%) each of Burkholderia pseudomallei and Streptococcus agalactiae. Of 70 Enterobacteriaceae, 62 (88.6%) were fluoroquinolone-resistant. Among 27 E. coli and K. pneumoniae, 18 (66.6%) were extended-spectrum beta-lactamase (ESBL)-producers, and 1 (3.7%) each were AmpC beta-lactamase- and carbapenemase-producers. Fluoroquinolone resistance was associated predominantly with mutations in the quinolone resistance-determining region. blaCTX-M-15 expression was common among ESBL-producers. Methicillin-resistant S. aureus was not detected. Fluoroquinolone-resistant, but not multiple drug-resistant, typhoidal S. enterica was the leading cause of community-onset BSI at a tertiary hospital in Yangon, Myanmar. Fluoroquinolone and extended-spectrum cephalosporin resistance was common among other Enterobactericeae. Our findings inform empiric management of severe febrile illness in Yangon and indicate that measures to prevent and control enteric fever are warranted. We suggest ongoing monitoring and efforts to mitigate antimicrobial resistance among community-onset pathogens.

Pharmacological Interventions for Bacterial Prostatitis

Prostatitis is a common urinary tract condition but bring innumerable trouble to clinicians in treatment, as well as great financial burden to patients and the society. Bacterial prostatitis (acute bacterial prostatitis plus chronic bacterial prostatitis) accounting for approximately 20% among all prostatitis have made the urological clinics complain about the genital and urinary systems all over the world. The international challenges of antibacterial treatment (emergence of multidrug-resistant bacteria, extended-spectrum beta-lactamase-producing bacteria, bacterial biofilms production and the shift in bacterial etiology) and the transformation of therapeutic strategy for classic therapy have attracted worldwide attention. To the best of our knowledge currently, there is not a single comprehensive review, which can completely elaborate these important topics and the corresponding treatment strategy in an effective way. This review summarizes the general treatment choices for bacterial prostatitis also provides the alternative pharmacological therapies for those patients resistant or intolerant to general treatment.

Multidrug-Resistant Bacterial Infections in U.S. Hospitalized Patients, 2012-2017

BACKGROUND

Multidrug-resistant (MDR) bacteria that are commonly associated with health care cause a substantial health burden. Updated national estimates for this group of pathogens are needed to inform public health action.

METHODS

Using data from patients hospitalized in a cohort of 890 U.S. hospitals during the period 2012-2017, we generated national case counts for both hospital-onset and community-onset infections caused by methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococcus (VRE), extended-spectrum cephalosporin resistance in Enterobacteriaceae suggestive of extended-spectrum beta-lactamase (ESBL) production, carbapenem-resistant Enterobacteriaceae, carbapenem-resistant acinetobacter species, and MDR Pseudomonas aeruginosa.

RESULTS

The hospital cohort in the study accounted for 41.6 million hospitalizations (>20% of U.S. hospitalizations annually). The overall rate of clinical cultures was 292 cultures per 1000 patient-days and was stable throughout the time period. In 2017, these pathogens caused an estimated 622,390 infections (95% confidence interval [CI], 579,125 to 665,655) among hospitalized patients. Of these infections, 517,818 (83%) had their onset in the community, and 104,572 (17%) had their onset in the hospital. MRSA and ESBL infections accounted for the majority of the infections (52% and 32%, respectively). Between 2012 and 2017, the incidence decreased for MRSA infection (from 114.18 to 93.68 cases per 10,000 hospitalizations), VRE infection (from 24.15 to 15.76 per 10,000), carbapenem-resistant acinetobacter species infection (from 3.33 to 2.47 per 10,000), and MDR P. aeruginosa infection (from 13.10 to 9.43 per 10,000), with decreases ranging from -20.5% to -39.2%. The incidence of carbapenem-resistant Enterobacteriaceae infection did not change significantly (from 3.36 to 3.79 cases per 10,000 hospitalizations). The incidence of ESBL infection increased by 53.3% (from 37.55 to 57.12 cases per 10,000 hospitalizations), a change driven by an increase in community-onset cases.

CONCLUSIONS

Health care-associated antimicrobial resistance places a substantial burden on patients in the United States. Further work is needed to identify improved interventions for both the inpatient and outpatient settings. (Funded by the Centers for Disease Control and Prevention.).

Imipenemase-producing carbapenem-resistant Enterobacteriaceae transmission in a long-term-care facility during a community-wide multidrug resistant organism outbreak-North Carolina, 2017

We describe an outbreak of imipenemase metallo-β-lactamase-producing organisms in a long-term-care facility (LTCF) amid a larger community outbreak of extended-spectrum β-lactamase-producing organisms. Transmission was propagated by inadequate infection prevention practices. We provided infection prevention recommendations and education, facilitated colonization screening, and increased interfacility communication. This outbreak demonstrates the unmet need for infection prevention education in long-term-care facilities and the importance of prompt public health response to ensure appropriate identification, containment, and prevention of emerging resistance.

Global Evolution of Pathogenic Bacteria With Extensive Use of Fluoroquinolone Agents

It is well-established that the spread of many multidrug-resistant (MDR) bacteria is predominantly clonal. Interestingly the international clones/sequence types (STs) of most pathogens emerged and disseminated during the last three decades. Strong experimental evidence from multiple laboratories indicate that diverse fitness cost associated with high-level resistance to fluoroquinolones contributed to the selection and promotion of the international clones/STs of hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA), extended-spectrum β-lactamase-(ESBL)-producing Klebsiella pneumoniae, ESBL-producing Escherichia coli and Clostridioides difficile. The overwhelming part of the literature investigating the epidemiology of the pathogens as a function of fluoroquinolone use remain in concordence with these findings. Moreover, recent in vitro data clearly show the potential of fluoroquinolone exposure to shape the clonal evolution of Salmonella Enteritidis. The success of the international clones/STs in all these species was linked to the strains' unique ability to evolve multiple energetically beneficial gyrase and topoisomerase IV mutations conferring high-level resistance to fluorquinolones and concomittantly permitting the acquisition of an extra resistance gene load without evoking appreciable fitness cost. Furthermore, by analyzing the clonality of multiple species, the review highlights, that in environments under high antibiotic exposure virulence factors play only a subsidiary role in the clonal dynamics of bacteria relative to multidrug-resistance coupled with favorable fitness (greater speed of replication). Though other groups of antibiotics should also be involved in selecting clones of bacterial pathogens the role of fluoroquinolones due to their peculiar fitness effect remains unique. It is suggested that probably no bacteria remain immune to the influence of fluoroquinolones in shaping their evolutionary dynamics. Consequently a more judicious use of fluoroquinolones, attuned to the proportion of international clone/ST isolates among local pathogens, would not only decrease resistance rates against this group of antibiotics but should also ameliorate the overall antibiotic resistance landscape.

Prevalence and Molecular Characteristics of Extended-Spectrum and AmpC β-Lactamase Producing Escherichia coli in Grazing Beef Cattle

The emergence of extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase producing Escherichia coli represent a contemporary public health threat. ESBL and AmpC β-lactamase genes translocate between chromosomes and plasmids, facilitating rapid spread throughout the environment. In this study, ESBL/AmpC producing bacteria were isolated from beef cattle farms with seldom antibiotic use. Eleven farms out of 17 tested, had ESBL/AmpC producing E. coli in animals, soil, and forage samples. Fifty-nine CTX-M or CMY-2 positive E. coli isolates were further characterized with whole-genome sequencing. The isolates commonly carried CMY-2, TEM, or CTX-M genes, and over half encoded both CTX-M and TEM genes. Using comparative genomics, antimicrobial resistance genes from 12 classes of antimicrobial were identified and confirmed by antibiotic susceptibility test, revealing multidrug resistance against multiple classes of antibiotics. Virulence factors related to adherence, invasion, iron uptake, and bacterial secretion systems were shared by all isolates; some of which were identified as enteropathogenic E. coli. Phylogenetic analyses revealed a pattern of close genetic relatedness, suggesting that ESBL/AmpC producing E. coli were transmitted among farms as well as independent evolution within farms. Our results indicate that ESBL and AmpC β-lactamases prevail in food animal production system regardless antibiotic use and have the characteristics for zoonotic transmission.

Short or Long Antibiotic Regimes in Orthopaedics (SOLARIO): a randomised controlled open-label non-inferiority trial of duration of systemic antibiotics in adults with orthopaedic infection treated operatively with local antibiotic therapy

BACKGROUND

Orthopaedic infections, such as osteomyelitis, diabetic foot infection and prosthetic joint infection, are most commonly treated by a combination of surgical debridement and a prolonged course of systemic antibiotics, usually for at least 4-6 weeks. Use of local antibiotics, implanted directly into the site of infection at the time of surgery, may improve antibiotic delivery and allow us to shorten the duration of systemic antibiotic therapy, thereby limiting the frequency of side effects, cost and selection pressure for antimicrobial resistance.

METHODS

SOLARIO is a multicentre open-label randomised controlled non-inferiority trial comparing short and long systemic antibiotic therapy alongside local antibiotic therapy. Adult patients with orthopaedic infection, who have given informed consent, will be eligible to participate in the study provided that no micro-organisms identified from deep tissue samples are resistant to locally implanted antibiotics. Participants will be randomised in a 1:1 ratio to receive either a short course (≤ 7 days) or currently recommended long course (≥ 4 weeks) of systemic antibiotics. The primary outcome will be treatment failure by 12 months after surgery, as ascertained by an independent Endpoint Committee blinded to treatment allocation. An absolute non-inferiority margin of 10% will be used for both per-protocol and intention-to-treat populations. Secondary outcomes will include probable and definite treatment failure, serious adverse events, treatment side effects, quality of life scores and cost analysis.

DISCUSSION

This study aims to assess a treatment strategy that may enable the reduction of systemic antibiotic use for patients with orthopaedic infection. If this strategy is non-inferior, this will be to the advantage of patients and contribute to antimicrobial stewardship.

TRIAL REGISTRATION

Clinicaltrials.gov, NCT03806166. Registered on 11 November 2019.

Clinical outcomes of urinary tract infection caused by extended spectrum beta-lactamase producing Enterobacteriaceae: a retrospective observational study comparing patients with and without systemic inflammatory response syndrome

Aim

In severe urinary tract infection (UTI), susceptible antibiotics should be given. With the recent increase of multidrug‐resistant bacteria, especially extended spectrum beta‐lactamase producing Enterobacteriaceae (ESBL‐E), broad‐spectrum antibiotics, such as carbapenems, are used more frequently, which could lead to a further increase of multidrug‐resistant bacteria. We aimed to analyze the relationship between initial empirical antibiotic appropriateness and clinical outcomes in UTI, especially in patients with systemic inflammatory response syndrome (SIRS) and ESBL‐E.

Methods

A retrospective observational study from 2012 to 2017.

Results

Among urine culture‐positive cases with ≥10⁵ colony‐forming units/mL (n = 1,880), true UTI cases were extracted (n = 844) and divided into the SIRS group (n = 336 [ESBL‐E12.8% (43/336)]) and non‐SIRS group (n = 508 [ESBL‐E12.6% (64/508)]). In the SIRS ESBL‐E group, the initial antibiotics were susceptible in 55.8% (24/43), among which 91.7% (22/24) improved and 8.3% (2/24) deteriorated or died. The initial antibiotics were resistant in 44.2% (19/43), among which 47.4% (9/19) improved with the initial antibiotics, 47.4% (9/19) improved after escalating antibiotics, and 5.3% (1/19) deteriorated or died. In the SIRS group, 14 cases had true bacteremia with ESBL‐E. Seven cases were initiated with inappropriate antibiotics; four cases showed improvement before or without antibiotic change and three cases improved after antibiotic escalation.

Conclusion

Initiation of narrow‐spectrum antibiotics in septic UTI with ESBL‐E might not deteriorate the clinical outcome if promptly escalated on clinical deterioration or with ESBL‐E culture results. Further investigation is warranted to guide judicious use of initial antibiotics.

Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly

BACKGROUND

Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT). Our ability to understand how certain organisms attain intestinal domination over others has been restricted in part by current metagenomic sequencing technologies that are typically unable to reconstruct complete genomes for individual organisms present within a sequenced microbial community. We recently developed a metagenomic read cloud sequencing and assembly approach that generates improved draft genomes for individual organisms compared to conventional short-read sequencing and assembly methods. Herein, we applied metagenomic read cloud sequencing to four stool samples collected longitudinally from an HCT patient preceding treatment and over the course of heavy antibiotic exposure.

RESULTS

Characterization of microbiome composition by taxonomic classification of reads reveals that that upon antibiotic exposure, the subject's gut microbiome experienced a marked decrease in diversity and became dominated by Escherichia coli. While diversity is restored at the final time point, this occurs without recovery of the original species and strain-level composition. Draft genomes for individual organisms within each sample were generated using both read cloud and conventional assembly. Read clouds were found to improve the completeness and contiguity of genome assemblies compared to conventional assembly. Moreover, read clouds enabled the placement of antibiotic resistance genes present in multiple copies both within a single draft genome and across multiple organisms. The occurrence of resistance genes associates with the timing of antibiotics administered to the patient, and comparative genomic analysis of the various intestinal E. coli strains across time points as well as the bloodstream isolate showed that the subject's E. coli bloodstream infection likely originated from the intestine. The E. coli genome from the initial pre-transplant stool sample harbors 46 known antimicrobial resistance genes, while all other species from the pre-transplant sample each contain at most 5 genes, consistent with a model of heavy antibiotic exposure resulting in selective outgrowth of the highly antibiotic-resistant E. coli.

CONCLUSION

This study demonstrates the application and utility of metagenomic read cloud sequencing and assembly to study the underlying strain-level genomic factors influencing gut microbiome dynamics under extreme selective pressures in the clinical context of HCT.

Genomic Surveillance Reveals Diversity of Multidrug-Resistant Organism Colonization and Infection: A Prospective Cohort Study in Liver Transplant Recipients

Background

Multidrug-resistant organisms (MDROs) are an important cause of morbidity and mortality after solid organ transplantation. We aimed to characterize MDRO colonization dynamics and infection in liver transplant (LT) recipients through innovative use of active surveillance and whole-genome sequencing (WGS).

Methods

We prospectively enrolled consecutive adult patients undergoing LT from March 2014 to March 2016. Fecal samples were collected at multiple timepoints from time of enrollment to 12 months posttransplant. Samples were screened for carbapenem-resistant Enterobacteriaceae (CRE), Enterobacteriaceae resistant to third-generation cephalosporins (Ceph-RE), and vancomycin-resistant enterococci. We performed WGS of CRE and selected Ceph-RE isolates. We also collected clinical data including demographics, transplant characteristics, and infection data.

Results

We collected 998 stool samples and 119 rectal swabs from 128 patients. MDRO colonization was detected in 86 (67%) patients at least once and was significantly associated with subsequent MDRO infection (0 vs 19.8%, P = .002). Child-Turcotte-Pugh score at LT and duration of post-LT hospitalization were independent predictors of both MDRO colonization and infection. Temporal dynamics differed between MDROs with respect to onset of colonization, clearance, and infections. We detected an unexpected diversity of CRE colonizing isolates and previously unrecognized transmission that spanned Ceph-RE and CRE phenotypes, as well as a cluster of mcr-1-producing isolates.

Conclusions

Active surveillance and WGS showed that MDRO colonization is a highly dynamic and complex process after LT. Understanding that complexity is crucial for informing decisions regarding MDRO infection control, use of therapeutic decolonization, and empiric treatment regimens.

The higher prevalence of extended spectrum beta-lactamases among Escherichia coli ST131 in Southeast Asia is driven by expansion of a single, locally prevalent subclone

The ST131 multilocus sequence type (MLST) of Escherichia coli is a globally successful pathogen whose dissemination is increasing rates of antibiotic resistance. Numerous global surveys have demonstrated the pervasiveness of this clone; in some regions ST131 accounts for up to 30% of all E. coli isolates. However, many regions are underrepresented in these published surveys, including Africa, South America, and Asia. We collected consecutive bloodstream E. coli isolates from three countries in Southeast Asia; ST131 was the most common MLST type. As in other studies, the C2/H30Rx clade accounted for the majority of ST131 strains. Clinical risk factors were similar to other reported studies. However, we found that nearly all of the C2 strains in this study were closely related, forming what we denote the SEA-C2 clone. The SEA-C2 clone is enriched for strains from Asia, particularly Southeast Asia and Singapore. The SEA-C2 clone accounts for all of the excess resistance and virulence of ST131 relative to non-ST131 E. coli. The SEA-C2 strains appear to be locally circulating and dominant in Southeast Asia, despite the intuition that high international connectivity and travel would enable frequent opportunities for other strains to establish themselves.

Abundance and Antimicrobial Resistance of Three Bacterial Species along a Complete Wastewater Pathway

After consumption, antibiotic residues and exposed bacteria end up via the feces in wastewater, and therefore wastewater is believed to play an important role in the spread of antimicrobial resistance (AMR). We investigated the abundance and AMR profiles of three different species over a complete wastewater pathway during a one-year sampling campaign, as well as including antimicrobial consumption and antimicrobial concentrations analysis. A total of 2886 isolates (997 Escherichia coli, 863 Klebsiella spp., and 1026 Aeromonas spp.) were cultured from the 211 samples collected. The bacterial AMR profiles mirrored the antimicrobial consumption in the respective locations, which were highest in the hospital. However, the contribution of hospital wastewater to AMR found in the wastewater treatment plant (WWTP) was below 10% for all antimicrobials tested. We found high concentrations (7-8 logs CFU/L) of the three bacterial species in all wastewaters, and they survived the wastewater treatment (effluent concentrations were around 5 log CFU/L), showing an increase of E. coli in the receiving river after the WWTP discharge. Although the WWTP had no effect on the proportion of AMR, bacterial species and antimicrobial residues were still measured in the effluent, showing the role of wastewater contamination in the environmental surface water.

Comparative Genomics of Antibiotic-Resistant Uropathogens Implicates Three Routes for Recurrence of Urinary Tract Infections

The rise of antimicrobial resistance in uropathogens has complicated the management of urinary tract infections (UTIs), particularly in patients who are afflicted by recurrent episodes of UTIs. Antimicrobial-resistant (AR) uropathogens persistently colonizing individuals at asymptomatic time points have been implicated in the pathophysiology of UTIs. The dynamics of uropathogen persistence following the resolution of symptomatic disease are, however, mostly unclear. To further our understanding, we determined longitudinal AR uropathogen carriage and clonal persistence of uropathogenic Escherichia coli, Proteus mirabilis, and Klebsiella pneumoniae isolates in the intestinal and urinary tracts of patients affected by recurrent and nonrecurrent UTIs. Clonal tracking of isolates in consecutively collected urine and fecal specimens indicated repeated transmission of uropathogens between the urinary tract and their intestinal reservoir. Our results further implicate three independent routes of recurrence of UTIs: (i) following an intestinal bloom of uropathogenic bacteria and subsequent bladder colonization, (ii) reinfection of the urinary tract from an external source, and (iii) bacterial persistence within the urinary tract. Taken together, our observation of clonal persistence following UTIs and uropathogen transmission between the intestinal and urinary tracts warrants further investigations into the connection between the intestinal microbiome and recurrent UTIs.IMPORTANCE The increasing antimicrobial resistance of uropathogens is challenging the continued efficacy of empiric antibiotic therapy for UTIs, which are among the most frequent bacterial infections worldwide. It has been suggested that drug-resistant uropathogens could persist in the intestine after the resolution of UTI and cause recurrences following periurethral contamination. A better understanding of the transmission dynamics between the intestinal and urinary tracts, combined with phenotypic characterization of the uropathogen populations in both habitats, could inform prudent therapies designed to overcome the rising resistance of uropathogens. Here, we integrate genomic surveillance with clinical microbiology to show that drug-resistant clones persist within and are readily transmitted between the intestinal and urinary tracts of patients affected by recurrent and nonrecurrent UTIs. Thus, our results advocate for understanding persistent intestinal uropathogen colonization as part of the pathophysiology of UTIs, particularly in patients affected by recurrent episodes of symptomatic disease.

Risk factors for community acquired urinary tract infections caused by extended spectrum β-lactamase (ESBL) producing Escherichia coli in children: a case control study

Background: We noted a recent increase in cases of urinary tract infection due to community-acquired ESBL-producing Escherichia coli in children treated at our institution. Risk factors of urinary tract infection due to ESBL-producing E. coli in children in the USA remain unclear. Methods: A single center retrospective case control study of UTI due to CA-ESBL-producing E. coli during a 5-year period (2012-2016). Control cases with non-ESBL-producing E. coli urinary tract infection were matched by age, gender and year of infection. Results: A total of 111 patients with ESBL-producing E coli urinary tract infection and 103 controls were included. The proportion of ESBL-producing E coli urinary tract infection ranged from 7% to 15% of all UTI cases. The distribution of ESBL cases per year: 27 in 2012; 18 in 2013; 22 in 2014; 15 in 2015 and 29 in 2016. Median age was 4 years with female predominance (84%). The ESBL group was predominantly African American (32%) followed by individuals of Middle Eastern ethnic background (31%). Risk factors by univariate analysis were vesicoureteral reflux: (20.9 ESBL group vs 6% controls; p = .002), prior antibiotic usage in the last 3 months (including β-lactams), prior UTI (last 3 months), recent hospitalization (last 3 months) and Middle Eastern ethnic background. However, multivariate analysis showed that only prior antibiotic usage (p = .001) and Middle Eastern ethnic background (p < .001) were independent risk factors. ESBL-producing strains were more frequently resistant to trimethoprim-sulfamethoxazole (72% vs 25%) and ciprofloxacin (73% vs 5%) than strains not producing ESBL. Conclusion: Risk factors for community-acquired ESBL-producing E coli urinary tract in our pediatric patient population were antibiotic usage within the previous 3 months and Middle Eastern ethnic background. This may be related to increased risk of intestinal colonization with resistant bacterial strains.

Noncarbapenems for the Treatment of Urinary Tract Infections Caused by Extended-Spectrum β-Lactamase-Producing Bacteria

OBJECTIVES

Urinary tract infections (UTIs) caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are resistant to many conventional therapies, including third-generation cephalosporins. Carbapenems are considered first-line agents for ESBL infections, but their use is associated with increased multidrug resistance and should be reserved when absolutely necessary. Because of the increased rates of UTIs caused by ESBL-producing organisms and incidence of carbapenem resistance, safe and effective alternatives to carbapenems are needed. This study was conducted to evaluate the outcomes associated with the treatment of ESBL UTIs with noncarbapenem antibiotics.

METHODS

A retrospective cohort study of adults with ESBL UTIs was conducted at a community hospital. Patients were categorized as those receiving definitive carbapenem therapy and those receiving definitive noncarbapenem therapy. Calculated measurements included infection-related mortality, length of hospital stay, and duration of definitive antibiotic therapy. Microbiological failure was assessed as a secondary outcome. Data on the safety of antibiotic therapy were not collected. P < 0.05 was considered significant.

RESULTS

Fifty patients met inclusion criteria for the study, divided evenly between the two cohorts. No statistical differences were observed for length of hospital stay (P = 0.601), duration of therapy (P = 0.398), or rate of microbiological failure between the groups (P = 0.115).

CONCLUSIONS

Noncarbapenems did not demonstrate significant differences compared with carbapenems in the treatment of adults with ESBL UTIs. In certain patient populations, noncarbapenems that demonstrate in vitro activity may be appropriate for UTIs caused by ESBL-producing organisms.

The Relative Impact of Community and Hospital Antibiotic Use on the Selection of Extended-spectrum Beta-lactamase-producing Escherichia coli

Antibiotic stewardship programs have traditionally focused on reducing hospital antibiotic use. However, reducing community antibiotic prescribing could have substantial impacts in both hospital and community settings. We developed a deterministic model of transmission of extended-spectrum beta-lactamase-producing Escherichia coli in both the community and hospitals. We fit the model to existing, national-level antibiotic use and resistance prevalence data from Sweden. Across a range of conditions, a given relative change in antibiotic use in the community had a greater impact on resistance prevalence in both the community and hospitals than an equivalent relative change in hospital use. However, on a per prescription basis, changes in antibiotic use in hospitals had the greatest impact. The magnitude of changes in prevalence were modest, even with large changes in antimicrobial use. These data support the expansion of stewardship programs/interventions beyond the walls of hospitals, but also suggest that such efforts would benefit hospitals themselves.

Trends in antimicrobial resistance in Israel, 2014-2017

We analyzed Israeli national data on antimicrobial susceptibility from bloodstream isolates collected between 2014 and 2017 and compared resistance proportions with those of Europe. The incidence of bloodstream infection (BSI) caused by most antibiotic-resistant organisms remained unchanged or decreased. An exception was increased incidence of BSI caused by third-generation cephalosporin-resistant Escherichia coli. Overall, resistance proportions were similar to those observed in southern Europe, with the exception of a lower proportion of carbapenem-resistant Klebsiella pneumoniae in Israel.

Antimicrobial Activity Evaluation of Tebipenem (SPR859), an Orally Available Carbapenem, against a Global Set of Enterobacteriaceae Isolates, Including a Challenge Set of Organisms

The antimicrobial activity of tebipenem and other carbapenem agents were tested in vitro against a set of recent clinical isolates responsible for urinary tract infection (UTI), as well as against a challenge set. Isolates were tested by reference broth microdilution and included Escherichia coli (101 isolates), Klebsiella pneumoniae (208 isolates), and Proteus mirabilis (103 isolates) species. Within each species tested, tebipenem showed equivalent MIC_50/90 values to those of meropenem (E. coli MIC_50/90, ≤0.015/0.03 mg/liter; K. pneumoniae MIC_50/90, 0.03/0.06 mg/liter; and P. mirabilis MIC_50/90, 0.06/0.12 mg/liter) and consistently displayed MIC₉₀ values 8-fold lower than imipenem. Tebipenem and meropenem (MIC₅₀, 0.03 mg/liter) showed equivalent MIC₅₀ results against wild-type, AmpC-, and/or extended-spectrum β-lactamase (ESBL)-producing isolates. Tebipenem also displayed MIC_50/90 values 4- to 8-fold lower than imipenem against the challenge set. All carbapenem agents were less active (MIC₅₀, ≥8 mg/liter) against isolates carrying carbapenemase genes. These data confirm the in vitro activity of the orally available agent tebipenem against prevalent UTI Enterobacteriaceae species, including those producing ESBLs and/or plasmid AmpC enzymes.

Influence of primary care antibiotic prescribing on incidence rates of multidrug-resistant Gram-negative bacteria in hospitalised patients

PURPOSE

Use of antibiotics can give rise to the selection of resistant bacteria. It remains unclear whether antibiotic use in primary care can influence bacterial resistance incidence in patients when hospitalised. The aim of this study is to explore the impact of prior community antibiotic usage on hospital-detected multidrug-resistant Gram-negative (MRGN) incidence rate.

METHODS

This pharmacoepidemiological study was case-control in design, and was carried out in the Antrim Area Hospital (N. Ireland) in two phases. In phase 1, the controls were matched according to: age, gender, admission ward, date of admission, and age-adjusted Charlson co-morbidity index score. During the second phase, controls were selected randomly from the total population of admissions to the hospital over the 2-year study period.

RESULTS

In phase 1, multivariate analysis revealed that prior exposure to the second- and third-generation cephalosporins (p = 0.004) and fluoroquinolones (p = 0.023) in primary care was associated with an increased likelihood of MRGN detection in inpatients. In phase 2, an independent relationship between an increased risk of identification of MRGN, while hospitalised was associated with: prolonged hospitalisation (p < 0.001), being elderly (p < 0.001), being female (p = 0.007), and having genitourinary disease (p < 0.001).

CONCLUSION

This study provides clear evidence which supports the need to optimise antibiotic use in primary care to help reduce MRGN incidence in hospitalised patients.

Whole genome analysis of cephalosporin-resistant Escherichia coli from bloodstream infections in Australia, New Zealand and Singapore: high prevalence of CMY-2 producers and ST131 carrying blaCTX-M-15 and blaCTX-M-27

Objectives

To characterize MDR Escherichia coli from bloodstream infections (BSIs) in Australia, New Zealand and Singapore.

Methods

We collected third-generation cephalosporin-resistant (3GC-R) E. coli from blood cultures in patients enrolled in a randomized controlled trial from February 2014 to August 2015. WGS was used to characterize antibiotic resistance genes, MLST, plasmids and phylogenetic relationships. Antibiotic susceptibility was determined using disc diffusion and Etest.

Results

A total of 70 3GC-R E. coli were included, of which the majority were ST131 (61.4%). BSI was most frequently from a urinary source (69.6%), community associated (62.9%) and in older patients (median age 71 years). The median Pitt score was 1 and ICU admission was infrequent (3.1%). ST131 possessed more acquired resistance genes than non-ST131 (P = 0.003). Clade C1/C2 ST131 predominated (30.2% and 53.5% of ST131, respectively) and these were all ciprofloxacin resistant. All clade A ST131 (n = 6) were community associated. The predominant ESBL types were blaCTX-M (80.0%) and were strongly associated with ST131 (95% carried blaCTX-M), with the majority blaCTX-M-15. Clade C1 was associated with blaCTX-M-14 and blaCTX-M-27, whereas blaCTX-M-15 predominated in clade C2. Plasmid-mediated AmpC genes (mainly blaCMY-2) were frequent (17.1%) but were more common in non-ST131 (P < 0.001) isolates from Singapore and Brisbane. Two strains carried both blaCMY-2 and blaCTX-M. The majority of plasmid replicon types were IncF.

Conclusions

In a prospective collection of 3GC-R E. coli causing BSI, community-associated Clade C1/C2 ST131 predominate in association with blaCTX-M ESBLs, although a significant proportion of non-ST131 strains carried blaCMY-2.

A Clinical Prediction Tool for Extended-Spectrum Cephalosporin Resistance in Community-Onset Enterobacterales Urinary Tract Infection

Background

Bacterial resistance to first line antibiotics used to treat community-onset urinary tract infections (UTIs) continues to increase. We sought to create a clinical prediction tool for community-onset UTIs due to extended-spectrum cephalosporin-resistant (ESC-R) Enterobacterales (formerly Enterobacteriaceae, EB).

Methods

A case-control study was performed. The source population included patients presenting to an emergency department (ED) or outpatient practice with an EB UTI between 2010 and 2013. Case patients had ESC-R EB UTIs. Control patients had ESC-susceptible EB UTIs and were matched to cases 1:1 on study year. Multivariable conditional logistic regression was performed to develop the predictive model by maximizing the area under the receiver-operating curve (AUC). Internal validation was performed via bootstrapping.

Results

A total of 302 patients with a community-onset EB UTI were included, with 151 cases and 151 controls. After multivariable analysis, we found that presentation with an ESC-R EB community-onset UTI could be predicted by the following: (1) a history of malignancy; (2) a history of diabetes; (3) recent skilled nursing facility or hospital stay; (4) recent trimethoprim-sulfamethoxazole exposure; and (5) pyelonephritis at the time of presentation (AUC 0.73, Hosmer-Lemeshow goodness-of-fit P value 0.23). With this model, each covariate confers a single point, and a patient with ≥ 2 points is considered high risk for ESC-R EB (sensitivity 80%, specificity 54%). The adjusted AUC after bootstrapping was 0.71.

Conclusions

Community-onset ESC-R EB UTI can be predicted using the proposed scoring system, which can help guide diagnostic and therapeutic interventions.

Multi-state study of Enterobacteriaceae harboring extended-spectrum beta-lactamase and carbapenemase genes in U.S. drinking water

Community-associated acquisition of extended-spectrum beta-lactamase- (ESBL) and carbapenemase-producing Enterobacteriaceae has significantly increased in recent years, necessitating greater inquiry into potential exposure routes, including food and water sources. In high-income countries, drinking water is often neglected as a possible source of community exposure to antibiotic-resistant organisms. We screened coliform-positive tap water samples (n = 483) from public and private water systems in six states of the United States for bla_CTX-M, bla_SHV, bla_TEM, bla_KPC, bla_NDM, and bla_OXA-48-type genes by multiplex PCR. Positive samples were subcultured to isolate organisms harboring ESBL or carbapenemase genes. Thirty-one samples (6.4%) were positive for bla_CTX-M, ESBL-type bla_SHV or bla_TEM, or bla_OXA-48-type carbapenemase genes, including at least one positive sample from each state. ESBL and bla_OXA-48-type Enterobacteriaceae isolates included E. coli, Kluyvera, Providencia, Klebsiella, and Citrobacter species. The bla_OXA-48-type genes were also found in non-fermenting Gram-negative species, including Shewanella, Pseudomonas and Acinetobacter. Multiple isolates were phenotypically non-susceptible to third-generation cephalosporin or carbapenem antibiotics. These findings suggest that tap water in high income countries could serve as an important source of community exposure to ESBL and carbapenemase genes, and that these genes may be disseminated by non-Enterobacteriaceae that are not detected as part of standard microbiological water quality testing.

Genotypes and Antimicrobial Susceptibility Profiles of Hemolytic Escherichia coli from Diarrheic Piglets

Hemolytic Escherichia coli are important pathogens in neonatal and weaned pigs. In this study, we analyzed 95 hemolytic E. coli isolated from intestinal contents or fecal samples of diarrheic piglets in 15 states of the United States between November 2013 and December 2014. Phenotypic antimicrobial susceptibility was determined through Sensititre BOFO6F plates for all the strains. They were all resistant to clindamycin, penicillin, tiamulin, tilmicosin, and highly resistant to oxytetracycline (91.6%), chlortetracycline (78.9%), ampicillin (75.8%), and sulfadimethoxine (68.4%). 86.2% of them were multidrug resistant. Whole genome sequencing (WGS) showed that 55 strains were enterotoxigenic E. coli (ETEC) and 40 strains were non-ETEC, and the strains belonged to 22 known and 2 novel sequence types (STs). ST100 and ST10 were the main and predominant STs in ETEC strains, whereas the non-ETEC strains were diverse with ST23 and ST761 as the main STs. Antibiotic resistance gene/mutation profiling of the genomes confirmed the results of antimicrobial susceptibility test. Notably, significant differences were found in the susceptibility to enrofloxacin between ETEC and non-ETEC (58.2% vs. 5.0%) and gentamicin (32.7% vs. 7.5%). ampH, ampC2, and ampC1 were the most common beta-lactamase genes in all E. coli strains, and extended-spectrum beta-lactamase (ESBL) genes were rare in these isolates. This study provides new insights into antibiotic resistance and genotypes of intestinal pathogenic E. coli associated with swine disease in the United States, and support the utility of WGS in accurate prediction of resistance to most antibiotics.

Rapid Detection of Extended-Spectrum β-Lactamases (ESBL) and AmpC β-Lactamases in Enterobacterales: Development of a Screening Panel Using the MALDI-TOF MS-Based Direct-on-Target Microdroplet Growth Assay

Introduction: Antibiotic resistant bacteria are a growing concern worldwide. Extended-spectrum β-lactamases (ESBL) represent the most common resistance mechanism of Gram-negative bacteria against β-lactams, underlining the need for adequate diagnostic methods that provide reliable information in the shortest time possible. AmpC, a less prevalent but increasingly relevant class of β-lactamases, pose an additional challenge as their detection is complex. Here, we present an ESBL and AmpC screening panel employing the MALDI-TOF MS-based direct-on-target microdroplet growth assay (DOT-MGA). Materials and Methods: Four reference strains recommended by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) were used to develop the panel, which was further validated on 50 clinical Enterobacterales isolates resistant to third generation cephalosporins. The panel relies on the synergistic effect between ESBL and/or AmpC β-lactamase inhibitors and cephalosporins, which indicates β-lactamase production. Microdroplets containing the tested microorganism, cephalosporins in different concentrations and inhibitors were pipetted onto an MBT Biotarget and incubated for 3 or 4 h at 35 ± 1°C. Afterward, the liquid medium was removed and the material adhered to the spots was analyzed by MALDI-TOF MS. Synergy was detected by determining and comparing the minimum inhibitory concentrations of the tested cephalosporins with and without β-lactamase inhibitors. Data were interpreted following a diagnostic algorithm proposed by EUCAST in order to establish a final diagnosis. In comparison, PCR, broth microdilution (BMD) and combination disk tests (CDT) were performed. Results: Compared to the PCR results, the following positive and negative percent agreement values (PPA/NPA) were obtained for each resistance mechanism: ESBL, 94.44/100%; AmpC, 94.44/93.75% and ESBL+AmpC, 100/100%. These results, obtained after 4 h of incubation, were comparable with those of BMD and showed a higher accuracy than CDT. Discussion: We propose a novel phenotypic method for detection of ESBL and AmpC β-lactamases in Enterobacterales that provides reliable results in a short time, representing a promising alternative to the diagnostic techniques currently available. This easy-to-perform approach has potential for being implemented in routine laboratories, contributing to the further diversification of mass spectrometry technology into other fields such as antibiotic resistance testing.

Read cloud sequencing elucidates microbiome dynamics in a hematopoietic cell transplant patient

Low intestinal microbial diversity, often leading to domination of the intestine by a single organism, is associated with poor outcomes following hematopoietic cell transplantation (HCT). Understanding how certain organisms achieve domination in the intestine is limited by current metagenomic sequencing technologies, which are typically unable to reconstruct complete genome drafts without bacterial isolation and culture. Recently, we developed a metagenomic read cloud sequencing approach that provides significantly improved genome drafts for individual organisms compared to conventional short-read sequencing methods. Here, we apply read cloud sequencing to four longitudinal stool samples collected from an HCT patient before and after heavy antibiotic exposure. During this time period, the patient experienced Escherichia coli gut domination and an E. coli bloodstream infection. We find that read clouds enable the placement of multiple copies of antibiotic resistance genes both within and across genomes, and the presence of resistance genes correlates with the timing of antibiotics administered to the patient. Comparative genomic analysis reveals that the E. coli bloodstream infection likely originated from the gut. The pre-transplant E. coli genome harbors 46 known resistance genes, whereas all other organisms from the pre-transplant time point contain 5 or fewer resistance genes, supporting a model in which the E. coli outgrowth was a result of selection by heavy antibiotic exposure. This case study highlights the application of metagenomic read cloud sequencing in a clinical context to elucidate the genomic underpinnings of microbiome dynamics under extreme selective pressures.

Analysis of Risk Factors for Multiantibiotic-Resistant Infections Among Surgical Patients at a Children's Hospital

BACKGROUND

To identify the potential risk factors for multiantibiotic-resistant infections and provide sufficient evidence for multiantibiotic resistance prevention and control.

MATERIALS AND METHODS

We conducted a retrospective study of all patients in pediatric orthopedics, pediatric heart surgery, and pediatric general surgery at a level 3, grade A children's hospital from January to December 2016. The clinical laboratory information monitoring system and the medical record system were used to collect patient information regarding age, surgery type, preoperative length of stay, admission season, incision type, preoperative infection, intraoperative blood loss, postoperative use of invasive equipment, duration of catheter drainage, and timepoint of intraoperative prophylactic antibiotics administration. We used logistic univariate and multivariate regression analysis to analyze the potential risk factors for multiantibiotic-resistant infections among pediatric surgical patients. SPSS 21.0 and Excel software packages were used for the statistical analysis.

RESULTS

In total, 2,973 patients met the inclusion criteria: 1,247 patients in pediatric orthopedics, 1,089 patients in pediatric heart surgery, and 637 patients in pediatric general surgery. At the end of the study, 113 patients were multiantibiotic-resistant infection cases; the rate of multiantibiotic-resistant infections was 3.80%, and the detection rate was 84.79%. Multivariate analysis indicated that the multiantibiotic-resistant infection cases were influenced by age, department, admission season, incision type, preoperative infection, and duration of catheter drainage.

CONCLUSIONS

Age, department, admission season, incision type, preoperative infection, and duration of catheter drainage may provide possible evidence for prevention and control strategies of multiantibiotic-resistant infections.

Pharmacokinetics and Pharmacodynamics of β-Lactamase Inhibitors

Novel β-lactamase inhibitors have extended the reach of new and existing β-lactams against multidrug-resistant bacteria expressing β-lactamases. The efficacy of these combination therapeutics relies on a complex two-component pharmacodynamic (PD) system where the β-lactamase inhibitor inactivates the bacterial β-lactamase enzyme and frees the companion β-lactam to act against its penicillin-binding protein target. Despite considerable investigation into the pharmacokinetics (PK) and pharmacodynamics of β-lactams, the pharmacology of their companion β-lactamase inhibitors has only recently been rigorously explored. This review describes the diversity of β-lactamase enzymes, mechanisms of enzyme inhibition, and factors impacting the efficacy of clinically available β-lactamase inhibitors. Relevant PK differences among available inhibitors and the PK/PD properties of these agents are described independently of their companion β-lactams. In the modern era of antibiotic resistance, a comprehensive understanding of the pharmacology, PK, and PD of β-lactamase inhibitors is paramount to maximizing the therapeutic efficacy of existing β-lactam/β-lactamase inhibitor combinations and protecting novel agents in the drug development pipeline.

Recent advances in managing lower urinary tract infections

Urinary tract infections (UTIs) are among the most common bacterial infections. Traditionally, all symptomatic UTIs are tested and treated. The use of antibiotics has resulted in an antibiotic resistance crisis, and we have limited options for managing UTIs. Currently, we live in the era of antimicrobial resistance and may live in other eras like the era of the microbiome. New insights might provide an opportunity to prevent the overuse and misuse of antibiotics and could enable the development of innovate managing strategies.

Risk Factors for Community-Acquired Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae Infections-A Retrospective Study of Symptomatic Urinary Tract Infections

Background

Community-acquired extended-spectrum beta-lactamase–producing Enterobacteriaceae (ESBL) infections are an evolving public health problem. Identifying predictive risk factors may improve patient management.

Methods

We identified 251 adult inpatients admitted to a 22-hospital system with an ESBL urinary tract infection (UTI) between 2001 and 2016. Cases were matched 1:1 with controls who had a UTI at admission with non-ESBL Enterobacteriaceae. Cases with a history of ESBL infections or hospitalization within 3 months of index admission were excluded. Univariate and multiple logistic regression were used to identify risk factors associated with ESBL UTIs.

Results

In univariate analysis, history of repeated UTIs, neurogenic bladder, urinary catheter presence at admission, and exposure to outpatient third-generation cephalosporins or fluoroquinolones within 3 months were associated with higher risk of ESBL UTIs. When controlling for severity of illness and comorbid conditions, history of repeated UTIs (adjusted odds ratio [aOR], 6.40; 95% confidence interval [CI], 3.42–12.66; P < .001), presence of urinary catheter at admission (aOR, 2.36; 95% CI, 1.15–4.98; P < .05), and prior antibiotic exposure (aOR, 7.98; 95% CI, 2.92–28.19; P < .001) remained associated with risk of ESBL infection.

Conclusions

Patients in the community with indwelling urinary catheters, history of recurrent UTIs, or recent antimicrobial use are at higher risk for de novo ESBL Enterobacteriaceae UTIs.

Trends in South Korean antimicrobial use and association with changes in Escherichia coli resistance rates: 12-year ecological study using a nationwide surveillance and antimicrobial prescription database

The purpose of this study is to determine the correlation between use of antimicrobials, such as fluoroquinolone, cefoxitin, and cefotaxime, and Escherichia coli resistance using a nationwide database. Nationwide data on antimicrobial consumption for 12 years (2002 to 2013) were acquired from a database of subjects (n = 1,025,340) included in the National Health Insurance Service-National Sample Cohort. National antimicrobial resistance rates of E. coli were obtained from the Korean Antimicrobial Resistance Monitoring System, which has been administered by the Korean Centers for Disease Control and Prevention since 2002. Fluoroquinolone-resistance rates of E. coli isolated from general hospitals have continuously increased since 2002 and were correlated with nationwide fluoroquinolone use (r = 0.82, P = 0.0012) or ciprofloxacin use (r = 0.90, P<0.0001). Cefotaxime-resistance rates of E. coli isolated from general hospitals markedly increased since 2008 and were correlated with nationwide cefotaxime use (r = 0.94, P<0.0001) or third-generation cephalosporin use (r = 0.96, P<0.0001). Cefoxitin-resistance rates of E. coli isolated from general hospitals peaked in 2010 and significantly correlated with cephamycin use at a two-year interval (r = 0.64, P = 0.0256). In conclusion, consumption of antimicrobials such as fluoroquinolone, cefoxitin, and cefotaxime is well correlated with the resistance rates of E. coli to these agents. This study provides background data for national antimicrobial management policies to reduce antimicrobial resistance.

Outpatient ertapenem therapy in an ESBL-high-prevalence area: an efficacy, safety, and cost study

Introduction

Outpatient parenteral antimicrobial therapy is a safe, effective, and convenient way of administering antimicrobials for a wide variety of infections. So far there are no reports on the efficacy of outpatient antimicrobial therapy in Mexico. Our objective was to determine the outcomes, safety, and cost of outpatient ertapenem therapy (OET) in our hospital.

Patients and methods

A case series of 99 patients that received intravenous OET was conducted. The primary outcomes were clinical cure, relapse, and recurrence of infection.

Results

Of the 99 patients who received OET the most common diagnosis was urinary tract infection in 56%. Extended-spectrum-β-lactamase-producing Enterobacteriaceae caused 67% of infections in our population. Ninety-seven percent of the patients were cured at the completion of OET. One patient presented relapse 12 days after the end of OET; two patients presented recurrence, one with skin and soft tissue infection and one with pyelonephritis at days 35 and 34, respectively, after the end of OET. Three patients were readmitted after OET, one with an episode of phlebitis, one with recurrence, and one with relapse. A case of non-Clostridium difficile-associated diarrhea was observed. The intravascular line complications observed during OET were phlebitis in two patients.

Conclusion

In our hospital, the OET was found to be effective, safe, and cost-saving when compared to inpatient care.

Post-appendectomy pelvic abscess with extended-spectrum beta-lactamase producing Escherichia coli: A case report and review of literature

BACKGROUND

Appendicitis, the inflammation of the appendix, is the most common abdominal surgical emergency requiring expedient surgical intervention. Extended-spectrum beta-lactamases (ESBLs) are bacterial enzymes that catalyse the degradation of the beta-lactam ring of penicillins and cephalosporins (but without carbapenemase activity), leading to resistance of these bacteria to beta-lactam antibiotics. Recent increases in incidence of ESBL-producing bacteria have caused alarm worldwide. Proportion estimates of ESBL-Enterobacteriaceae hover around 46% in China, 42% in East Africa, 12% in Germany, and 8% in the United States.

CASE SUMMARY

The impact of ESBL-producing bacteria on appendiceal abscesses and consequent pelvic abscesses are yet to be examined in depth. A literature review using the search words “appendiceal abscesses” and “ESBL Escherichia coli (E. coli)” revealed very few cases involving ESBL E. coli in any capacity in the context of appendiceal abscesses. This report describes the clinical aspects of a patient with appendicitis who developed a postoperative pelvic abscess infected with ESBL-producing E. coli. In this report, we discuss the risk factors for contracting ESBL E. coli infection in appendicitis and post-appendectomy pelvis abscesses. We also discuss our management approach for post-appendectomy ESBL E. coli pelvic abscesses, including drainage, pathogen identification, and pathogen characterisation. When ESBL E. coli is confirmed, carbapenem antibiotics should be promptly administered, as was done efficaciously with this patient. Our report is the first one in a developed country involving ESBL E. coli related surgical complications in association with a routine laparoscopic appendectomy.

CONCLUSION

Our report is the first involving ESBL E. coli and appendiceal abscesses, and that too consequent to laparoscopic appendectomy.

Molecular characterization, antimicrobial resistance and clinico-bioinformatics approaches to address the problem of extended-spectrum β-lactamase-producing Escherichia coli in western Saudi Arabia

The goal of this study was to genotypically characterize extended-spectrum β-lactamase-producing Escherichia coli isolates from the western region of Saudi Arabia and to identify active antibiotics against these isolates using phenotypic and molecular modeling. In total, 211 ESBL-producing E. coli isolates recovered from heterogeneous clinical specimens were identified by MALDI-TOF. Thirty-two sequence types (STs) were identified from a multilocus sequence typing (MLST) analysis of ESBL-producing E. coli, including a novel ST (ST8162). The most common ST in the Saudi and expatriate population was ST131, followed by ST38. All the isolates were multidrug resistant (MDR), and >95% of the isolates were resistant to third-generation (ceftriaxone and ceftazidime) and fourth-generation (cefepime) cephalosporins. The ESBL-positive E. coli isolates primarily harbored the bla_CTX-M and bla_TEM genes. No resistance was observed against the carbapenem antibiotic group. All the ESBL-producing E. coli isolates were observed to be susceptible to a ceftazidime/avibactam combination. Molecular interaction analyses of the docked complexes revealed the amino acid residues crucial for the binding of antibiotics and inhibitors to the modeled CTX-M-15 enzyme. Importantly, avibactam displayed the most robust interaction with CTX-M-15 among the tested inhibitors in the docked state (∆G = −6.6 kcal/mol). The binding free energy values for clavulanate, tazobactam and sulbactam were determined to be −5.7, −5.9 and −5.2 kcal/mol, respectively. Overall, the study concludes that ‘ceftazidime along with avibactam’ should be carefully used as a treatment option against only carbapenem-resistant MDR ESBL-producing E. coli in this region.

Early-Onset Neonatal Sepsis with Extended Spectrum Beta-Lactamase Producing Escherichia Coli in Infants Born to South and South East Asian Immigrants: A Case Series

Extended-spectrum β -lactamase (ESBL)-producing Enterobacteriaceae represent a major worldwide threat. We present three cases of early onset ESBL Escherichia coli sepsis in infants born to families from South and Southeast Asia to inform the practitioner community about this emerging threat. Infants with suspected sepsis, whose mother is from Asia or Southeast Asia, should be suspected of having an infection with an ESBL-producing organism, and practitioners should strongly consider adding a carbapenem to their usual initial antibiotic regimen.