Application of Next-Generation Sequencing for Characterization of Surveillance and Clinical Trial Isolates: Analysis of the Distribution of β-lactamase Resistance Genes and Lineage Background in the United States

β-lactam resistant phenotypes reported by VITEK®2 advanced expert systemTM (AES) compared to whole genome sequencing in Enterobacterales from North and Latin America

The VITEK®2 AES β-lactam phenotypes of 488 Enterobacterales from North and Latin America generated by the VITEK®2 were compared to the resistance genotypes provided by whole genome sequencing (WGS). The AES provided phenotypic reports for 447 (91.6 %) isolates, including isolates harbouring carbapenemases (195; 43.6 %), ESBLs (103; 23.0 %) and transferable AmpCs (tAmpC; 28; 6.3 %) genes, as well as wildtype isolates (WT; 121; 27.1 %). Overall, the AES report was accurate for 433/447 (96.9 %) isolates. The AES accurately reported carbapenemase, ESBL, and tAmpC phenotypes for 93.7 %, 93.7 %, and 98.4 % of isolates, respectively, and sensitivity/specificity rates were 96.4 %/91.7 %, 98.1 %/92.4 %, 82.1 %/99.5 %, and 100 %/98.8 %. 14 isolates carrying carbapenemase (7 total; 3 KPC, 2 MBL, 2 OXA-48-like), ESBL (2), and tAmpC-encoding genes (5) were not correctly identified by AES. The AES phenotypic report detected resistance mechanisms among Enterobacterales rapidly and could significantly aid future antimicrobial stewardship initiatives and patient care.

Patient outcomes by baseline pathogen resistance phenotype and genotype in CERTAIN-1, a Phase 3 study of cefepime-taniborbactam versus meropenem in adults with complicated urinary tract infection

CERTAIN-1 was a Phase 3, double-blind, randomized, parallel group study of the efficacy and safety of cefepime-taniborbactam versus meropenem in the treatment of adults with complicated urinary tract infection (cUTI), including acute pyelonephritis. We determined susceptibility of Enterobacterales and Pseudomonas aeruginosa baseline pathogens to cefepime-taniborbactam and comparators and characterized β-lactam resistance mechanisms. Microbiologic response and clinical response were assessed in patient subsets defined by baseline pathogens that were of cefepime-, multidrug-, or carbapenem-resistant phenotype or that carried β-lactamase genes. Among Enterobacterales baseline pathogens, 26.8%, 4.1%, and 3.0% carried genes for extended-spectrum β-lactamases (ESBLs), AmpC, and carbapenemases, respectively. Within each treatment group, while composite success rates at Test of Cure in resistant subsets by pathogen species were similar to those by pathogen overall, composite success rates in meropenem patients were numerically lower for cefepime-resistant Escherichia coli (9/19; 47.4%) and ESBL E. coli (13/25; 52.0%) compared with E. coli overall (62/100; 62.0%). Cefepime-taniborbactam achieved composite success in 7/8 (87.5%) patients with carbapenem-resistant Enterobacterales and 8/9 (88.9%) patients with Enterobacterales with a carbapenemase gene (5 OXA-48-group; 2 KPC-3; 2 NDM-1). Cefepime-taniborbactam also achieved composite success in 8/16 (50.0%) patients and clinical success in 13/16 (81.3%) patients with P. aeruginosa; corresponding rates were 4/7 (57.1%) and 6/7 (85.7%) for meropenem. Cefepime-taniborbactam demonstrated efficacy in adult cUTI patients with cefepime-, multidrug-, and carbapenem-resistant pathogens including pathogens with ESBL, AmpC, and carbapenemase genes.

CLINICAL TRIALS

This study is registered with ClinicalTrials.gov as NCT03840148.

Epidemiology, clinical outcomes and risk factors of third-generation cephalosporin-resistant Escherichia coli hospitalized infections in remote Australia-a case-control study

Background

Incidence of third-generation cephalosporin-resistant (3GCR) Escherichia coli infections has increased in remote Australia from 2012 to 2018.

Objectives

To describe the epidemiology of 3GCR E. coli in Central Australia.

Methods

A case-control study was conducted in the primary Central Australian hospital. Patient characteristics, antibiotic usage and clinical outcomes were compared between adult hospitalizations with 3GCR and susceptible E. coli isolates in 2018-19. Poisson regression was used to compare the incidence of 3GCR hospitalizations between Indigenous and non-Indigenous individuals. Patient characteristics and antibiotic usage were tested for associations with 3GCR isolates using univariate analysis.

Results

A total of 889 E. coli isolates were identified, of which 187 (21%) were 3GCR. The incidence of 3GCR E. coli infection was 2.15 per 1000 person-years, with an incidence rate ratio of 6.8 (95% CI 4.6-10.1) between Indigenous and non-Indigenous individuals. When compared with the control group, 3GCR E. coli infections were associated with a higher Charlson comorbidity index (CCI ≥3 in 30.7% versus 15.0%, P < 0.001) and were more commonly healthcare associated (52.4% versus 26.7%, P < 0.001). A higher 1 year mortality was observed in the 3GCR group after adjustment for comorbidity (OR = 4.43, P = 0.002), but not at 30 days (2.4% versus 0.0%, P = 0.2). The 3GCR group used more antibiotics in the past 3 months (OR = 5.75, P < 0.001) and 12 months (OR = 3.65, P < 0.001).

Conclusions

3GCR E. coli infections in remote Australia disproportionally affect Indigenous peoples and are associated with a high burden of comorbidities and antibiotic use. Strategies to enhance antimicrobial stewardship should be considered in this remote setting.

Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission?

IMPORTANCE

Extraintestinal pathogenic Escherichia coli (ExPEC) sequence type (ST) 38 is one of the top 10 human pandemic lineages. Although a major cause of urinary tract and blood stream infections, ST38 has been poorly characterized from a global phylogenomic perspective. A comprehensive genome-scale analysis of 925 ST38 isolate genomes identified two broad ancestral clades and linkage of discrete ST38 clusters with specific bla CTX-M variants. In addition, the clades and clusters carry important virulence genes, with diverse but poorly characterized plasmids. Numerous putative interhost and environment transmission events were identified here by the presence of ST38 clones (defined as isolates with ≤35 SNPs) within humans, companion animals, food sources, urban birds, wildlife, and the environment. A small cluster of international ST38 clones from diverse sources, likely representing progenitors of a hospital outbreak that occurred in Brisbane, Australia, in 2017, was also identified. Our study emphasizes the importance of characterizing isolate genomes derived from nonhuman sources and geographical locations, without any selection bias.

Significant increase of CTX-M-15-ST131 and emergence of CTX-M-27-ST131 Escherichia coli high-risk clones causing healthcare-associated bacteraemia of urinary origin in Spain (ITUBRAS-2 project)

OBJECTIVES

To assess the microbiological characteristics of Escherichia coli causing healthcare-associated bacteraemia of urinary origin (HCA-BUO) in Spain (ITUBRAS-2 project), with particular focus on ESBL producers and isolates belonging to ST131 high-risk clone (HiRC). Clinical characteristics and outcomes associated with ST131 infection were investigated.

METHODS

A total of 222 E. coli blood isolates were prospectively collected from patients with HCA-BUO from 12 tertiary-care hospitals in Spain (2017-19). Antimicrobial susceptibility and ESBL/carbapenemase production were determined. ST131 subtyping was performed. A subset of 115 isolates were selected for WGS to determine population structure, resistome and virulome. Clinical charts were reviewed.

RESULTS

ESBL-producing E. coli prevalence was 30.6% (68/222). ST131 represented 29.7% (66/222) of E. coli isolates and accounted for the majority of ESBL producers (46/68, 67.6%). The C2/H30-Rx subclone accounted for most ST131 isolates (44/66) and was associated with CTX-M-15 (37/44) and OXA-1 enzymes (27/44). Cluster C1-M27 was identified in 4/10 isolates belonging to subclade C1/H30-R1 and associated with CTX-M-27. Additionally, ST131 isolates showed a high content of other acquired resistance genes, and clade C/ST131 isolates carried characteristic QRDR mutations. They were categorized as uropathogenic E. coli and had higher aggregate virulence scores. ST131 infection was associated with more complex patients, prior use of cephalosporins and inadequate empirical treatment but was not associated with worse clinical outcomes.

CONCLUSIONS

ST131 HiRC is the main driver of ESBL-producing E. coli causing HCA-BUO in Spain, mainly associated with the expansion of subclade CTX-M-15-C2/H30-Rx and the emergence of CTX-M-27-C1/H30-R1 (Cluster C1-M27).

Clinical and Epidemiological Characteristics of Carbapenem-Resistant Klebsiella pneumoniae Infections in a Tertiary Hospital in China

Purpose: Infections caused by carbapenem-resistant Klebsiella pneumoniae (CR-KP) are an important public health problem. This study aimed to evaluate the clinical characteristics of patients with CR-KP. Methods: A retrospective cohort study was conducted of all patients with CR-KP infection. A total of 615 patients with CR-KP infection were identified and 135 patients who did not meet the eligibility criteria were excluded. Clinical characteristics, antimicrobial regimens, and patient outcomes were analyzed. Results: The overall mortality rate of CR-KP infections was 37.3% and the mortality rate in patients with bloodstream infections was 66.2%. Survival analysis revealed that there were statistically significant differences between patients with bloodstream infections and those with pulmonary and drainage fluid infections. Logistics regression analysis showed that hemopathy, age >60 years, solid tumors, diabetes, septic shock, acute kidney injury, and stroke were independent predictors of 30-day mortality rate. The chi-square test showed that treatment with a combination of carbapenems, tigecycline, and polymyxin B was superior to treatment with carbapenems with polymyxin B, without tigecycline. Conclusions: CR-KP infections, especially bloodstream infections, have a high mortality rate. The outcome is strongly dependent on patients' clinical conditions. Antimicrobial regimens combining carbapenems, tigecycline, and polymyxin B might be a better choice.

High prevalence of β-lactam and fluoroquinolone resistance in various phylotypes of Escherichia coli isolates from urinary tract infections in Jiroft city, Iran

BACKGROUND

Urinary tract infection (UTI) is one of the most prevalent infectious diseases with worldwide health threatening. Antimicrobial resistant strains of Escherichia coli (E. coli) are a common cause of UTI which were identified as a treatment challenge. This study aimed to assay the prevalence of common β-lactam resistance genes including bla_TEM, bla_SHV, bla_CTX-M and bla_CMY and phenotypic resistance to commonly used β-lactam and fluoroquinolone antibiotics in UTIs. These factors were evaluated in various phylogenetic groups (phylotypes) of E. coli isolates. Real-time PCR was applied to detect β-lactam resistance genes and conventional PCR was used to determine the phylotypes. Phenotypic resistance against β-lactams (ceftazidime, cefotaxime, aztreonam and ceftriaxone) and fluoroquinolones (ciprofloxacin) were identified by the disc diffusion technique. The ability of extended spectrum β-lactamases (ESBLs) production in E. coli isolates was detected using the combined disc diffusion method.

RESULTS

The prevalence of resistance genes were 89.6% for bla_TEM, 44.3% for bla_CTX-M, 6.6% for bla_SHV and 0.9% for bla_CMY. The two high prevalent phylotypes were B2 (29.2%) and D (17.9%) followed by E (14.1%), F (9.4%), C (6.6%) and 10.3% of isolates were unknown in phylotyping. Disc diffusion results showed high prevalence of antibiotic resistance to cefotaxime (88.6%), aztreonam (83%), ceftireaxon (77.3%), ceftazidime (76.4%) and ciprofloxacin (55.6%). Totally, 52.8% of isolates were found as phenotypical ESBL-producers.

CONCLUSIONS

This study's results confirmed an explosion of antibiotic resistance amongst E. coli isolates from UTI against β-lactams and fluoroquinolones. Findings explain the necessity of deep changes in quantity and quality of drug resistance diagnosis and antibiotic therapy strategies. More studies are suggested to better and confident evaluations.

The Characteristics of Extended-Spectrum β-Lactamases (ESBLs)-Producing Escherichia coli in Bloodstream Infection

Background

Bloodstream infection (BSI) is a common type of infection frequently diagnosed in clinics. The emergence and spread of ESBLs-producing Escherichia coli (E. coli) has emerged as one of the biggest challenges in global community health.

Methods

The production of ESBLs was determined by the composite disk diffusion method. The expression of the various resistance and virulence genes were detected by PCR and sequencing. Multi-locus sequence typing (MLST) and phylogenetic groups were used for the classification. The transfer of resistant plasmids was determined by conjugation assay. The statistical differences were analyzed using Statistical Product and Service Solutions (SPSS) version 23.0.

Results

A total of 60 strains of ESBLs-producing E. coli were collected. The resistance genes that were identified included bla _CTX-M, bla _TEM, bla _SHV, bla _OXA-1 and mcr-1. The most common one was the bla _CTX-M including bla _CTX-M-27 (n = 16), bla _CTX-M-14 (n = 15), bla _CTX-M-15 (n = 11), bla _CTX-M-55 (n = 14) and bla _CTX-M-65 (n = 5). A total of 31 STs were detected, and the most abundant among which was ST131 (n = 16, 26.7%). Most of the E. coli (n = 46, 76.7%) belonged to the groups B2 and D. And some virulence genes were related to the classification of the E. coli. Among them, the detection rates of hek/hra, kpsMII and papGII-III in groups B2 and D were higher than those in groups A and B1. The detection rates of cnf1, iucC and papGII-III in ST131 were higher than those in non-ST131. And the distributions of hek/hra, iroN, iucC, kpsMII and papGII-III were related to the bla _CTX-M subtypes. Finally, most bacterial (n = 32, 53.3%) resistance genes could be transferred between the bacteria by plasmids, especially IncFIB.

Conclusion

ESBLs-producing E. coli in BSI exhibited had high resistance rates and carried a variety of virulence factors (VFs). This is necessary to strengthen the monitoring of ESBLs-producing isolates in the medical environment.

Performance of the Vitek 2 Advanced Expert System (AES) as a Rapid Tool for Reporting Antimicrobial Susceptibility Testing (AST) in Enterobacterales from North and Latin America

This study evaluated the performance of the Vitek 2 Advanced Expert System (AES) confidence level report as a rapid tool for reporting antimicrobial susceptibility testing (AST) results for a challenging set of Enterobacterales isolates from North and Latin America. Enterobacterales isolates (n = 513) were tested by CLSI broth microdilution (BMD) and Vitek 2 (N802 and XN15 AST cards). Wild-type isolates and isolates harboring acquired β-lactamases by whole-genome sequencing were included. The AES assessment of confidence level (green, yellow, and red reports) was compared to BMD results and known genotypes and reviewed by a microbiologist for accuracy. Totals of 148 (28.8%) wild-type isolates and 365 (71.2%) Enterobacterales isolates harboring carbapenemase (211 [41.1%]), extended-spectrum β-lactamase (ESBL) (122 [23.8%]), and/or transferrable AmpC (tAmpC) (32 [6.2%]) genes were evaluated. The AES confidence level was assessed for 488 isolates, and a phenotype was recognized for 447 (91.6%) isolates. Green, yellow, and red AES reports were noted for 382 (78.3%), 65 (13.3%), and 41 (8.4%) isolates, respectively. Compared to BMD, 96.3% of green AES reports could be confidently and rapidly auto-released, enabling rapid adjustments to antimicrobial therapy. In addition, 69.2% of yellow reports were acceptable, and recommendations to address current AES limitations were made. IMPORTANCE Antimicrobial susceptibility testing (AST) reports are one of the most important clinical microbiology laboratory tasks. AST reports are essential to drive antimicrobial therapy, provide information to monitor antimicrobial resistance rates, and trigger further tests to detect outbreaks or confirm new mechanisms of resistance. Commercial AST devices are frequently used to generate AST reports, and an advanced expert system (AES), such as the Vitek 2 AES, incorporates extensive knowledge to recognize certain susceptibility patterns as indicative of specific phenotypes. Moreover, the Vitek 2 AES also provides a level of confidence for auto-releasing the reports. In this study, the performance of the Vitek 2 AES was compared to state-of-the-art methodologies for AST, broth microdilution and β-lactamase gene detection, whole-genome sequencing, against a collection of 513 Enterobacterales clinical isolates harboring various β-lactamase genes, including carbapenemase, ESBL, and transferrable AmpC genes, from 73 medical centers in 7 countries in North and Latin America.

Impact of the Recent Clinical and Laboratory Standards Institute Breakpoint Changes on the Antimicrobial Spectrum of Aminoglycosides and the Activity of Plazomicin Against Multidrug-Resistant and Carbapenem-Resistant Enterobacterales From United States Medical Centers

Background

The Clinical and Laboratory Standards Institute (CLSI) lowered the Enterobacterales-susceptible/-resistant breakpoints for amikacin in 2023 from ≤16/≥64 mg/L to ≤4/≥16 mg/L and the breakpoints for gentamicin and tobramycin from ≤4/≥16 mg/L to ≤2/≥8 mg/L. Because aminoglycosides are frequently used to treat infections caused by multidrug-resistant (MDR) and carbapenem-resistant Enterobacterales (CRE), we evaluated the impact of these changes on the susceptibility rates (%S) of Enterobacterales collected from US medical centers.

Methods

A total of 9809 Enterobacterales isolates were consecutively collected (1/patient) from 37 US medical centers in 2017-2021 and susceptibility was tested by broth microdilution. Susceptibility rates were calculated using CLSI 2022, CLSI 2023, and US Food and Drug Administration 2022 criteria. Aminoglycoside-nonsusceptible isolates were screened for genes encoding aminoglycoside-modifying enzymes (AMEs) and 16S rRNA methyltransferases (16RMT).

Results

The CLSI breakpoint changes mostly affected amikacin, especially against MDR (94.0%S to 71.0%S), extended-spectrum β-lactamase (ESBL)-producing (96.9%S to 79.7%S), and CRE (75.2%S to 59.0%S) isolates. Plazomicin was active against 96.4% of isolates and retained potent activity against CRE (94.0%S), ESBL-producing (98.9%S), and MDR (94.8%S) isolates. Gentamicin and tobramycin showed limited activity against resistant subsets of Enterobacterales. The AME-encoding genes and 16RMT were observed in 801 (8.2%) and 11 (0.1%) isolates, respectively. Plazomicin was active against 97.3% of the AME producers.

Conclusions

The spectrum of activity of amikacin against resistant subsets of Enterobacterales was drastically reduced when interpretative criteria based on pharmacokinetic/pharmacodynamic parameters that are currently used to establish breakpoints for other antimicrobials were applied. Plazomicin was markedly more active than amikacin, gentamicin, or tobramycin against antimicrobial-resistant Enterobacterales.

Changing Epidemiology of Carbapenemases Among Carbapenem-Resistant Enterobacterales From United States Hospitals and the Activity of Aztreonam-Avibactam Against Contemporary Enterobacterales (2019-2021)

Background

As the frequency of metallo-β-lactamase (MBL)-producing Enterobacterales is increasing worldwide, effective antimicrobials to treat the infections caused by these organisms are urgently needed.

Methods

The activity of aztreonam-avibactam and comparators were evaluated against 27 834 Enterobacterales isolates collected from 74 US medical centers in 2019-2021. Isolates were susceptibility tested by broth microdilution. An aztreonam-avibactam pharmacokinetic/pharmacodynamic breakpoint of ≤8 mg/L was applied for comparison. Antimicrobial susceptibility and the frequency of key resistance phenotypes were assessed then stratified by year and infection type. Carbapenem-resistant Enterobacterales (CRE) were screened for carbapenemase (CPE) genes by whole genome sequencing.

Results

Aztreonam-avibactam inhibited >99.9% of Enterobacterales at ≤8 mg/L. Only 3 isolates (0.01%) had an aztreonam-avibactam minimum inhibitory concentration (MIC) >8 mg/L. The CRE rates were 0.8%, 0.9%, and 1.1% in 2019, 2020, and 2021, respectively; 99.6% (260 of 261) of CRE isolates were inhibited at an aztreonam-avibactam MIC of ≤8 mg/L. The CRE susceptibility to meropenem-vaborbactam decreased from 91.7% in 2019 to 83.1% in 2020 and 76.5% in 2021 (82.1% overall). The CRE, multidrug-resistant, and extensively drug-resistant phenotypes were markedly higher among isolates from pneumonia compared with other infections. The most common carbapenemase among CRE was Klebsiella pneumoniae carbapenemase (65.5% of CRE), followed by New Delhi metallo-β-lactamase (11.1%), oxacillinase (OXA)-48-like (4.6%), Serratia marcescens enzyme (2.3%), and imipenemase (1.5%). Among non-CPE-producing CRE isolates (n = 44; 16.9% of CRE), 97.7% were inhibited at ≤8 mg/L aztreonam-avibactam and 85.4% were meropenem-vaborbactam susceptible.

Conclusions

The frequencies of MBL and OXA-48-type producers increased markedly. Aztreonam-avibactam demonstrated potent and consistent activity against Enterobacterales across infection types and over time.

Bacterial Resistance in Hospital-Acquired Infections Acquired in the Intensive Care Unit: A Systematic Review

PURPOSE

In this review we present the status of the prevalence of bacteria resistant to antibiotics and the main antibiotic resistance genes that are reported in infections acquired in intensive care units (ICU) around the world.

METHODS

A systematic review based on the PRISMA guide was carried out, from the Science Direct, Redalyc, Scopus, Hinari, Scielo, Dialnet, PLOS, ProQuest, Taylor, Lilacs and PubMed/Medline databases. Inclusion criteria of this review were original research study published in a scientific journal in a 10-year time span from 1 January 2017 and 30 April 2022.

RESULTS

A total of 1686 studies were identified, but only 114 studies were considered eligible for inclusion. Klebsiella pneumoniae and Escherichia coli resistant to carbapenems and producers of extended-spectrum β-lactamases (ESBL) are the most frequently isolated pathogens in ICUs in Asia, Africa and Latin America. The blaOXA and blaCTX were antibiotic resistance genes (ARG) most commonly reported in different geographic regions (in 30 and 28 studies, respectively). Moreover, multidrug-resistant (MDR) strains were reported in higher frequency in hospital-acquired infections. Reports of MDR strains vary between continents, with the majority of publications being in Asia and between countries, with Egypt and Iran being highlighted. There is a predominance of few bacterial clones with MDR phenotype, for example, clonal complex 5 Methicillin-Resistant Staphylococcus aureus (CC5-MRSA) circulates frequently in hospitals in the United States, clone ST23-K. pneumoniae is reported in India and Iran, and clone ST260 carbapenemase-producing P. aeruginosa in the United States and Estonia.

CONCLUSION

Our systematic review reveals that ESBL- and carbapenemase-producing K. pneumoniae and E. coli are the most problematic bacteria that are reported, mainly in tertiary hospitals in Asia, Africa, and Latin America. We have also found propagation of dominant clones with a high degree of MDR, becoming a problem due to its high capacity to cause morbidity, mortality and additional hospital costs.

Know your Microbe Foes: The Role of Surveillance in Combatting Antimicrobial Resistance

Antibiotic-resistant organisms (AROs) are difficult and costly to treat, associated with high mortality rates, and are on the rise. In the United States, there is limited tracking of AROs, which can contribute to transmission and inhibit infection prevention interventions. Surveillance is limited by a lack of standardized methods for colonization screening and limited communication regarding patient ARO-status between healthcare settings. Some regional surveillance and reporting efforts are in place for extensively-resistant AROs such as carbapenem-resistant Enterobacterales (CRE), but need to be further expanded nationwide and to include other AROs such as extended-spectrum β-lactamase (ESBL) producing organisms. Increased surveillance of ARO infections and colonization will inform future targeted intervention and infection prevention strategies.

The plethora of resistance mechanisms in Pseudomonas aeruginosa: transcriptome analysis reveals a potential role of lipopolysaccharide pathway proteins to novel β-lactam/β-lactamase inhibitor combinations

OBJECTIVES

Whole genome and transcriptome analysis of 213 Pseudomonas aeruginosa isolates resistant to antipseudomonal β-lactams collected in 30 countries was performed to evaluate resistance mechanisms against these agents.

METHODS

Isolates were susceptibility tested by reference broth microdilution. Whole genome and transcriptome sequencing were performed, and data were analysed using open-source tools. A statistical analysis of changes in the expression of >5500 genes was compared to the expression of PAO1.

RESULTS

The high-risk clones ST235 and ST111 were the most prevalent among >90 sequence types (STs). Metallo-β-lactamase (MBLs) genes were detected in 40 isolates. AmpC and MexXY were the most common genes overexpressed in approximately 50% of the 173 isolates that did not carry MBLs. Isolates overexpressing pmrA and pmrB, the norspermidine production genes speD2 and speE2, and the operon arnBCADTEF-ugd were noted among strains resistant to ceftolozane-tazobactam and ceftazidime-avibactam, despite the lack of polymyxin resistance often associated to increased expression of these genes. Overexpression of MuxABC-OpmB, OprG, and OprE proteins were associated with resistance to ceftolozane-tazobactam in addition to the usual genes involved in cephalosporin, monobactam, and carbapenem resistance. Statistical analysis identified discrete mutations in ArmZ, OprD, and AmpC that correlated to antipseudomonal β-lactam resistance.

CONCLUSIONS

P. aeruginosa resistance mechanisms are complex. This analysis suggests the role of multiple genes in resistance to antipseudomonal β-lactams, including some not commonly described.

In Vitro Activity of Tebipenem against Various Resistant Subsets of Escherichia coli Causing Urinary Tract Infections in the United States (2018 to 2020)

This study investigated the activity of an oral carbapenem, tebipenem, against various molecularly characterized subsets of Escherichia coli. A total of 15.0% of E. coli isolates (360/2,035 isolates) met the MIC criteria for screening for β-lactamases. Most of those isolates (74.7% [269/360 isolates]) carried bla_CTX-M. The CTX-M distribution varied (50% to 86%) among Census Regions, as did that of plasmid AmpC genes (up to 41% among E. coli isolates from the New England Region). Tebipenem and intravenous carbapenems showed uniform activity against various E. coli subsets.

Antimicrobial activity of cefepime/zidebactam (WCK 5222), a β-lactam/β-lactam enhancer combination, against clinical isolates of Gram-negative bacteria collected worldwide (2018-19)

BACKGROUND

Zidebactam, a bicyclo-acyl hydrazide β-lactam 'enhancer' antibiotic, in combination with cefepime (WCK 5222) is under clinical development for the treatment of resistant Gram-negative infections.

OBJECTIVES

To evaluate the in vitro activity of cefepime/zidebactam and comparators against 24 220 Gram-negative bacteria.

METHODS

Organisms were consecutively collected in 2018-19 from 137 medical centres located in the USA (n = 9140), Western Europe (W-EU; n = 5929), Eastern Europe (E-EU; n = 3036), the Asia-Pacific region (APAC; n = 3791) and Latin America (LATAM; n = 2324). The isolates were susceptibility tested using the broth microdilution method as part of the SENTRY Program. Cefepime/zidebactam was tested at a 1:1 ratio.

RESULTS

Cefepime/zidebactam was highly active against Enterobacterales (MIC50/90 0.03/0.25 mg/L; 99.9% inhibited at ≤8 mg/L) and retained potent activity against carbapenem-resistant Enterobacterales (CRE) isolates (97.8% inhibited at ≤8 mg/L). CRE rates varied widely from 1.1% in the USA to 1.9% in W-EU, 3.6% in APAC and 14.6% in E-EU (3.9% overall). The most common carbapenemase genes observed overall were blaKPC (37.6% of CRE), blaOXA-48-like (30.0%) and blaNDM (23.8%). Resistance to ceftazidime/avibactam among CRE was elevated in APAC (64.8%), E-EU (25.5%) and LATAM (20.7%). Against Pseudomonas aeruginosa, cefepime/zidebactam inhibited 99.2% of isolates at ≤8 mg/L and susceptibility to ceftazidime/avibactam and ceftolozane/tazobactam was lowest in E-EU (83.9% and 82.0%, respectively). Cefepime/zidebactam exhibited good activity against Stenotrophomonas maltophilia (80.0% inhibited at ≤8 mg/L) and Burkholderia cepacia (89.4% inhibited at ≤8 mg/L).

CONCLUSIONS

Cefepime/zidebactam demonstrated potent in vitro activity against a large worldwide collection of contemporary clinical isolates of Gram-negative bacteria.

Ceftolozane/tazobactam for hospital-acquired/ventilator-associated bacterial pneumonia due to ESBL-producing Enterobacterales: a subgroup analysis of the ASPECT-NP clinical trial

BACKGROUND

After the MERINO trial with piperacillin/tazobactam, the efficacy of β-lactam/tazobactam combinations in serious infections involving extended-spectrum β-lactamase (ESBL)-producing pathogens merits special evaluation.

OBJECTIVES

To further confirm the efficacy of ceftolozane/tazobactam in treating hospital-acquired/ventilator-associated bacterial pneumonia (HABP/VABP) involving ESBL-positive and/or AmpC-producing Enterobacterales.

METHODS

Retrospective subgroup analysis of the ASPECT-NP trial comparing ceftolozane/tazobactam with meropenem for treating HABP/VABP in mechanically ventilated adults (ClinicalTrials.gov NCT02070757). ESBLs were identified using whole genome sequencing. Chromosomal AmpC production was quantified employing a high-sensitivity mRNA transcription assay.

RESULTS

Overall, 61/726 (8.4%) participants had all baseline lower respiratory tract (LRT) isolates susceptible to both study treatments and ≥1 baseline ESBL-positive/AmpC-overproducing Enterobacterales isolate. In this subgroup (ceftolozane/tazobactam n = 30, meropenem n = 31), baseline characteristics were generally comparable between treatment arms. The most frequent ESBL-positive and/or AmpC-overproducing Enterobacterales isolates (ceftolozane/tazobactam n = 31, meropenem n = 35) overall were Klebsiella pneumoniae (50.0%), Escherichia coli (22.7%), and Proteus mirabilis (7.6%). The most prevalent ESBLs were CTX-M-15 (75.8%), other CTX-M (19.7%), and SHV (4.5%); 10.6% of isolates overproduced chromosomal AmpC. Overall, 28 day all-cause mortality was 6.7% (2/30) with ceftolozane/tazobactam and 32.3% (10/31) with meropenem (25.6% difference, 95% CI: 5.54 to 43.84). Clinical cure rate at test-of-cure, 7-14 days after end of therapy, was 73.3% (22/30) with ceftolozane/tazobactam and 61.3% (19/31) with meropenem (12.0% difference, 95% CI: -11.21 to +33.51). Per-isolate microbiological response at test-of-cure was 64.5% (20/31) with ceftolozane/tazobactam and 74.3% (26/35) with meropenem (-9.8% difference, 95% CI: -30.80 to +12.00).

CONCLUSIONS

These data confirm ceftolozane/tazobactam as an effective treatment option for HABP/VABP involving ceftolozane/tazobactam-susceptible ESBL-positive and/or AmpC-producing Enterobacterales.

In vitro activity of imipenem/relebactam and comparator agents against clinical bacterial isolates from patients with cancer

BACKGROUND

Gram-negative bacilli (GNB) are currently the predominant bacterial pathogens in patients with cancer. Many GNB have become problematic due to the widespread emergence of resistance. Imipenem/relebactam (IMP/REL) is a combination of the carbapenem imipenem with relebactam, a non-beta-lactam beta-lactamase inhibitor. It is active against most pathogenic GNB including many that are resistant to other agents. We compared its in vitro activity to 6 other agents against 490 GNB recovered exclusively from patients with cancer, since such data are scarce.

METHODS

CLSI microbroth dilution methods were used for susceptibility testing. Whole genome sequencing (Illumina MiSeq) was performed on 30 selected isolates.

RESULTS

IMP/REL was active against 98 % of Enterobacterales and 87 % of non-Enterobacterales isolates (excluding Stenotrophomonas maltophilia). It had potent activity against ESBL-producing Escherichia coli and Klebsiella pneumoniae, and other Enterobacterales (Enterobacter cloacae, Citrobacter spp., and Serratia spp.), and moderate activity against carbapenem-resistant Enterobacterales. IMI/REL had potent activity against Achromobacter spp., non-MDR Pseudomonas aeruginosa, and Sphingomonas paucimobilis and moderate activity against MDR P. aeruginosa. Overall, imipenem/relebactam was associated with the lowest number of non-susceptible isolates compared to 6 other agents (imipenem, meropenem, cefepime, piperacillin/tazobactam, amikacin, and tigecycline) commonly used in cancer patients. Whole genome sequencing performed on 30 resistant isolates (10 each of E. coli, Klebsiella pneumonia, and P.aeruginosa) did not reveal any predominant mechanism of resistance to imipenem/relebactam.

CONCLUSION

Its in vitro activity indicates that IMI/REL might have a role to play for the treatment of Gram-negative infections in patients with cancer.

Antimicrobial activities of aztreonam-avibactam and comparator agents tested against Enterobacterales from European hospitals analysed by geographic region and infection type (2019-2020)

The purpose of this study is to evaluate the activities of aztreonam-avibactam and comparator agents against Enterobacterales isolates from European medical centres as well as the occurrence of carbapenemases (CPEs). A total of 11,655 Enterobacterales isolates were collected consecutively in 2019-2020 from 38 medical centres located in Western Europe (W-EU; n = 8,784; 25 centres in 10 countries) and the Eastern European and Mediterranean region (E-EU; n = 2,871; 13 centres in 10 countries). Isolates were susceptibility tested by broth microdilution methods in a monitoring laboratory. The antimicrobial susceptibility and frequency of key resistance phenotypes were assessed and stratified by geographic region and infection type. Isolates that showed resistance to carbapenems (CRE) and/or elevated MICs (> 8 mg/L) for aztreonam-avibactam were screened for β-lactamase-encoding genes by whole-genome sequencing. Aztreonam-avibactam inhibited 99.9% of Enterobacterales at ≤ 8 mg/L (MIC_50/90, ≤ 0.03/0.12 mg/L) and retained potent activity against CRE (MIC_50/90, 0.25/0.5 mg/L), multidrug-resistant isolates (MDR; MIC_50/90, 0.12/0.5 mg/L), and extensively drug-resistant (XDR) isolates (MIC_50/90, 0.25/0.5 mg/L). Susceptibility to comparator agents was consistently lower among isolates from E-EU compared to W-EU for all infection types evaluated. CRE rates varied from 0.6% (urinary tract infection [UTI]) to 2.3% (bloodstream infection) in W-EU, and from 6.1% (UTI) to 17.0% (pneumonia) in E-EU. A CPE-encoding gene was identified in 360 of 424 (84.9%) CRE isolates, and the most common CPEs were bla_KPC (36.3% of CRE), bla_OXA-48 type (27.1% of CRE), and the MBLs (25.7% of CRE). All CPE producers were inhibited at an aztreonam-avibactam concentration of ≤ 8 mg/L. Aztreonam-avibactam demonstrated potent activity across the evaluated geographic regions and infection types.

Challenge of evolving Klebsiella pneumoniae infection in patients on hemodialysis: from the classic strain to the carbapenem-resistant hypervirulent one

Loss of renal function may render hemodialysis patients more susceptible to infectious diseases, which is the second of all-causes mortality in this population. In addition to infection caused by the classic Klebsiella pneumoniae (cKp), however, hemodialysis staffs are now facing new challenge with growing prevalence of the carbapenem-resistant Kp (CR-Kp) and hypervirulent Kp (hvKp) as they are respectively associated with increased drug-resistance and virulence. We therefore chose to share our recent experience in treating severe infections either caused (cKp, CR-Kp, hvKp) or complicated (CR-hvKp) by these strains in hemodialysis patients. Based upon yet beyond published works, we further came up with the detection of intracranial lesion, novel diagnostic approach using unique biomarkers followed by selection of appropriate antibiotics, management of metastasic abscesses and bracing for the most lethal scenario in the order of cKp, CR-Kp, hvKp and CR-hvKp, respectively. Since reports of complicated hvKp infection in hemodialysis patients were rare, we also discussed in details this clinical entity focusing on its epidemiology, mechanism of increased virulence and involvement of the arteriovenous fistula as insidious source of persistent septicemia. By covering the full spectrum of clinically relevant Kp stains specifically from the viewpoint of nephrology, our work had highlighted the importance of infection control in uremic state and vice versa. As such, it may greatly raise the awareness of dialysis staffs against the challenge of evolving Klebsiella pneumoniae infection in hemodialysis patients and expeditiously reach a higher degree of readiness which was proved to be the key determinant of ultimate survival.

In vitro activity of a novel aminomethylcycline antibacterial (KBP-7072), a third-generation tetracycline, against clinical isolates with molecularly characterized tetracycline resistance mechanisms

Objectives

This study evaluated the in vitro activity of KBP-7072 against 413 contemporary surveillance isolates, including subsets with known tetracycline resistance genes.

Materials

In total, 105 Klebsiella pneumoniae (51 tetracycline resistant), 103 Escherichia coli (52 tetracycline resistant), 103 Staphylococcus aureus (51 tetracycline resistant) and 102 Streptococcus pneumoniae (51 tetracycline resistant) isolates were included. These isolates were tested by broth microdilution using fresh media. CLSI/EUCAST breakpoints were applied, except for tigecycline and omadacycline, which used FDA criteria.

Results

KBP-7072 (MIC₅₀, 0.06 mg/L), tigecycline (MIC₅₀, 0.12 and 0.25 mg/L) and omadacycline (MIC₅₀, 0.12 and 0.5 mg/L) showed similar MIC₅₀s for tetracycline-susceptible and -resistant S. aureus. Other tetracycline comparators had their MIC₅₀ increased 64- to 256-fold by tet. For S. pneumoniae, KBP-7072 (MIC_50/90, ≤0.015/0.03 mg/L) showed the lowest MICs, which remained unchanged for tetracycline-susceptible or -resistant isolates [mostly tet(M)]. Similar MICs were observed for omadacycline (MIC_50/90, 0.03–0.06/0.06 mg/L) and tigecycline (MIC_50/90, 0.03/0.03 mg/L) in the S. pneumoniae population. Tetracycline-susceptible and -resistant E. coli [94.2% tet(A)/tet(B)], KBP-7072 (MIC₉₀, 0.25 and 1 mg/L, respectively) and tigecycline (MIC₉₀, 0.25 and 0.5 mg/L) showed similar MIC₉₀s. KBP-7072 (MIC_50/90, 0.25/0.5 mg/L) and tigecycline (MIC_50/90, 0.5/0.5 mg/L) had the lowest MIC for tetracycline-susceptible K. pneumoniae. The MIC for KBP-7072 (MIC_50/90, 1/4 mg/L) and tigecycline (MIC_50/90, 1/2 mg/L) increased 2- to 8-fold for tetracycline-resistant K. pneumoniae, which mostly produced Tet(A).

Conclusions

KBP-7072 activity was minimally affected by the presence of acquired tetracycline genes.

In vitro activity of the orally bioavailable ceftibuten/VNRX-7145 (VNRX-5236 etzadroxil) combination against a challenge set of Enterobacterales pathogens carrying molecularly characterized β-lactamase genes

Objectives

This study assessed the activity of ceftibuten, ceftibuten combined with the active form (VNRX-5236) of the β-lactamase inhibitor VNRX-7145 and comparators against a challenge set of Gram-negative pathogens.

Methods

Two hundred and five Enterobacterales carrying plasmid AmpC (53 isolates), ESBL (50), KPC (50), OXA-48-like (49) or OXA-48-like with KPC (3) encoding genes were selected. Susceptibility was determined by broth microdilution. VNRX-5236 and avibactam were tested at a fixed concentration of 4 mg/L.

Results

Ceftibuten/VNRX-5236 (MIC_50/90 0.12/1 mg/L) MIC values were 256-fold lower than those of ceftibuten (MIC_50/90 32/256 mg/L) for all Enterobacterales and 2- to 4-fold lower than those of ceftazidime/avibactam (MIC_50/90 0.5/2 mg/L). For isolates producing a plasmid-encoded AmpC, VNRX-5236 decreased ceftibuten MIC (MIC_50/90 0.12/1 mg/L) by at least 512-fold compared with ceftibuten (MIC_50/90 128/>256 mg/L). Ceftibuten/VNRX-5236 (MIC_50/90 0.06/0.12 mg/L) and meropenem (MIC_50/90 ≤0.03/0.06 mg/L; 100% susceptible) showed comparable activities against ESBL isolates and these agents had MIC₉₀ values 4- to 8-fold lower than that of ceftazidime/avibactam (MIC_50/90 0.25/0.5 mg/L; 100% susceptible). Ceftibuten/VNRX-5236 (MIC_50/90 0.12/0.5 mg/L) had the lowest MIC for KPC producers, followed by ceftazidime/avibactam (MIC_50/90 2/4 mg/L; 98.0% susceptible). The same MIC₉₀ values were obtained for ceftibuten/VNRX-5236 (MIC_50/90 0.25/1 mg/L) and ceftazidime/avibactam (MIC_50/90 1/1 mg/L; 100.0% susceptible) for isolates carrying bla_OXA-48-like. VNRX-5236 decreased the ceftibuten MIC at least 16-fold for three isolates carrying bla_OXA-48-like and bla_KPC.

Conclusions

VNRX-5236 rescued the in vitro activity of ceftibuten against Enterobacterales carrying common serine β-lactamases, including ESBL, AmpC and the KPC and OXA-48-like carbapenemases. Ceftibuten/VNRX-5236 may have potential as an oral treatment for infections caused by resistant Enterobacterales, while sparing carbapenems.

Antimicrobial susceptibility of Gram-negative bacteria from intensive care unit and non-intensive care unit patients from United States hospitals (2018-2020)

We evaluated the antimicrobial susceptibility of Gram-negative bacteria recovered from ICU patients in US hospitals and compared them to those from non-ICU patients from the same hospitals during the same period. Overall, 4,680 isolates from ICU patients and 16,263 isolates from non-ICU patients were collected from 70 US medical centers in 2018-2020 and susceptibility tested by the broth microdilution method. Ceftazidime-avibactam and ceftolozane-tazobactam were the most active agents against P. aeruginosa and retained activity against multidrug-resistant (MDR) and extensively drug-resistant (XDR) isolates. Minocycline and trimethoprim-sulfamethoxazole were very active against S. maltophilia, whereas most antimicrobial agents exhibited low susceptibility to A. baumannii. Ceftazidime-avibactam and meropenem-vaborbactam were the most active agents against Enterobacterales, and retained potent activity against ESBL producers, carbapenem-resistant Enterobacterales (CRE), MDR, and XDR isolates. In summary, antimicrobial susceptibility was generally lower and the occurrence of ESBL, CRE, MDR, and XDR phenotypes were clearly higher among ICU compared to non-ICU isolates.

Investigation of mechanisms responsible for decreased susceptibility of aztreonam/avibactam activity in clinical isolates of Enterobacterales collected in Europe, Asia and Latin America in 2019

Background

The combination aztreonam/avibactam is currently under Phase 3 trials for the treatment of serious infections caused by Gram-negative bacteria including those with MBLs.

Objectives

To investigate the resistance mechanisms in Enterobacterales exhibiting aztreonam/avibactam MICs of ≥4 mg/L.

Methods

Among 8787 Enterobacterales, 17 (0.2%) isolates exhibited an aztreonam/avibactam MIC of ≥4 mg/L. Isolates were sequenced and screened for β-lactamases. Sequences of porins, penicillin-binding protein 3 (PBP3) and expression levels of AmpC and AcrA were evaluated.

Results

Eleven (11/4154 isolates; 0.26%) Escherichia coli, three (3/1981; 0.15%) Klebsiella pneumoniae and three (3/628; 0.5%) Enterobacter cloacae were identified. All E. coli showed either an ‘YRIK’ or ‘YRIN’ insertion in PBP3. In general, these isolates carried bla_CMY and/or bla_CTX-M variants, except for one isolate from Korea that also produced NDM-5 and one isolate from Turkey that produced OXA-48. Two DHA-1-producing K. pneumoniae overexpressed acrA and had a premature stop codon in either OmpK35 or OmpK36, whereas a third K. pneumoniae carried bla_PER-2 and had a premature stop codon in OmpK35. All three E. cloacae expressed AmpC at levels ≥570-fold, but sequence analysis did not reveal known amino acid alterations associated with decreased avibactam binding or increased hydrolysis of β-lactams. Minor amino acid polymorphisms within OmpC, OmpF and PBP3 were noted among the E. cloacae.

Conclusions

A small number of isolates (0.2%) met the inclusion criteria. E. coli showed altered PBP3 as the most relevant resistance mechanism, whereas K. pneumoniae had multiple resistance mechanisms. Further investigations are needed to clarify resistance in E. cloacae.

Extended-spectrum β-lactamases: an update on their characteristics, epidemiology and detection

Extended-spectrum β-lactamase (ESBL)-producing Gram-negative pathogens are a major cause of resistance to expanded-spectrum β-lactam antibiotics. Since their discovery in the early 1980s, they have spread worldwide and an are now endemic in Enterobacterales isolated from both hospital-associated and community-acquired infections. As a result, they are a global public health concern. In the past, TEM- and SHV-type ESBLs were the predominant families of ESBLs. Today CTX-M-type enzymes are the most commonly found ESBL type with the CTX-M-15 variant dominating worldwide, followed in prevalence by CTX-M-14, and CTX-M-27 is emerging in certain parts of the world. The genes encoding ESBLs are often found on plasmids and harboured within transposons or insertion sequences, which has enabled their spread. In addition, the population of ESBL-producing Escherichia coli is dominated globally by a highly virulent and successful clone belonging to ST131. Today, there are many diagnostic tools available to the clinical microbiology laboratory and include both phenotypic and genotypic tests to detect β-lactamases. Unfortunately, when ESBLs are not identified in a timely manner, appropriate antimicrobial therapy is frequently delayed, resulting in poor clinical outcomes. Several analyses of clinical trials have shown mixed results with regards to whether a carbapenem must be used to treat serious infections caused by ESBLs or whether some of the older β-lactam-β-lactamase combinations such as piperacillin/tazobactam are appropriate. Some of the newer combinations such as ceftazidime/avibactam have demonstrated efficacy in patients. ESBL-producing Gram-negative pathogens will continue to be major contributor to antimicrobial resistance worldwide. It is essential that we remain vigilant about identifying them both in patient isolates and through surveillance studies.

Distribution of β-Lactamase Genes in Clinical Isolates from California Central Valley Hospital Deviates from the United States Nationwide Trends

The evolution and dissemination of antibiotic resistance genes throughout the world are clearly affected by the selection and migration of resistant bacteria. However, the relative contributions of selection and migration at a local scale have not been fully explored. We sought to identify which of these factors has the strongest effect through comparisons of antibiotic resistance gene abundance between a distinct location and its surroundings over an extended period of six years. In this work, we used two repositories of extended spectrum β-lactamase (ESBL)-producing isolates collected since 2013 from patients at Dignity Health Mercy Medical Center (DHMMC) in Merced, California, USA, and a nationwide database compiled from clinical isolate genomes reported by the National Center for Biotechnology Information (NCBI) since 2013. We analyzed the stability of average resistance gene frequencies over the years since collection of these clinical isolates began for each repository. We then compared the frequencies of resistance genes in the DHMMC collection with the averages of the nationwide frequencies. We found DHMMC gene frequencies are stable over time and differ significantly from nationwide frequencies throughout the period of time we examined. Our results suggest that local selective pressures are a more important influence on the population structure of resistance genes in bacterial populations than migration. This, in turn, indicates the potential for antibiotic resistance to be controlled at a regional level, making it easier to limit the spread through local stewardship.

Characterization of a vga gene variant recovered from a Staphylococcus saprophyticus causing a community-acquired urinary tract infection: report from the SENTRY Antimicrobial Surveillance Program 2017

A patient with a history of UTI acquired an isolate of Staphylococcus saprophyticus that was resistant to clindamycin, streptogramin A, pleuromutilins (LSPs), and oxacillin. A plasmid-located vga variant was identified in this pathogen, and the encoded protein showed a 39% to 67% identity to other previously characterized vga.

Third-Generation Cephalosporin Resistance and Associated Discordant Antibiotic Treatment in Emergency Department Febrile Urinary Tract Infections

STUDY OBJECTIVE

Third-generation cephalosporin-resistant (3GCR) Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis (EKP) are an increasingly common cause of community-onset urinary tract infections (UTIs) in the United States. The 3GCR antimicrobial resistance pattern in these Enterobacterales species is most commonly due to production of extended-spectrum β-lactamases. We sought to provide contemporary, emergency department (ED)-focused data on 3GCR-EKP UTI regional prevalence, presentation, antibiotic susceptibility, and empiric treatment patterns, and outcomes.

METHODS

We performed a retrospective cohort study of all adults admitted with a febrile UTI at 21 Kaiser Permanente Northern California EDs between January 2017 and June 2019. Inclusion criteria included fever; admitting diagnosis of UTI, pyelonephritis, or sepsis; and ED urine culture with greater than 100,000 colony-forming units/mL of an EKP species. 3GCR was defined as in vitro resistance to ceftriaxone, ceftazidime, or both. 3GCR-EKP cases were compared with non-3GCR-EKP controls for the following: demographics, comorbidities, presenting clinical features, urinary isolate antimicrobial susceptibility, treatment, and clinical outcomes. The primary outcome measure was the rate of discordant initial empiric antibiotic treatment (administered within 6 hours of ED arrival) when compared with antimicrobial susceptibility testing. Secondary outcomes included hospital length of stay and 90-day mortality, adjusted for comorbidities and severity of illness.

RESULTS

There were 4,107 patients (median age 73 years and 35% men) who met study inclusion criteria. Of these patients, 530 (12.9%) had a 3GCR-EKP urinary tract infection. The proportion of subjects possessing risk factors for a health care-associated or extended-spectrum β-lactamase infection was 92.8% of case patients and 86.1% of controls. When comparing 3GCR-EKP case and non-3GCR-EKP control isolates, ciprofloxacin susceptibility rates were 21% versus 88%, and piperacillin/tazobactam susceptibility rates were 89% versus 97%, respectively. Initial empiric antibiotic therapy was discordant with antimicrobial susceptibility testing results in 63% of case patients versus 7% of controls (odds ratio 21.0; 95% confidence interval 16.9 to 26.0). The hospital length of stay was longer for 3GCR-EKP case patients, with an adjusted mean difference of 29.7 hours (95% CI 19.0 to 40.4). Ninety-day mortality was 12% in case patients versus 8% in controls (adjusted odds ratio 1.56; 95% confidence interval 1.07 to 2.28).

CONCLUSION

In this large, 2017 to 2019 Northern California ED study, nearly 13% of febrile EKP UTIs requiring hospitalization were caused by 3GCR-EKP, and in these cases, initial empiric therapy was often discordant with antimicrobial susceptibility testing. 3GCR-EKP infections were associated with a longer hospital length of stay and higher 90-day mortality. Similar data from other regions and for outpatient UTIs are needed.

Molecular Characterization of Baseline Enterobacterales and Pseudomonas aeruginosa Isolates from a Phase 3 Nosocomial Pneumonia (ASPECT-NP) Clinical Trial

We reviewed β-lactam-resistant baseline Enterobacterales species and Pseudomonas aeruginosa lower respiratory tract isolates collected during the ASPECT-NP phase 3 clinical trial that evaluated the safety and efficacy of ceftolozane-tazobactam compared with meropenem for the treatment of nosocomial pneumonia in ventilated adults. Isolates were subjected to whole-genome sequencing, real-time PCR for the quantification of the expression levels of β-lactamase and efflux pump genes, and Western blot analysis for the detection of OprD (P. aeruginosa only). Extended-spectrum β-lactamase (ESBL) genes were detected in 168 of 262 Enterobacterales isolates, and among these, bla _CTX-M-15 was the most common, detected in 125 isolates. Sixty-one Enterobacterales isolates carried genes encoding carbapenemases, while 33 isolates did not carry ESBLs or carbapenemases. Carbapenemase-producing isolates carried mainly NDM and OXA-48 variants, with ceftolozane-tazobactam MIC values ranging from 4 to 128 µg/ml. Most ceftolozane-tazobactam-nonsusceptible Enterobacterales isolates that did not carry carbapenemases were Klebsiella pneumoniae isolates that exhibited disrupted OmpK35, specific mutations in OmpK36, and, in some isolates, elevated expression of bla _CTX-M-15 Among 89 P. aeruginosa isolates, carbapenemases and ESBL-encoding genes were observed in 12 and 22 isolates, respectively. P. aeruginosa isolates without acquired β-lactamases displaying elevated expression of AmpC (14 isolates), elevated expression of efflux pumps (11 isolates), and/or a decrease or loss of OprD (22 isolates) were susceptible to ceftolozane-tazobactam. Ceftolozane-tazobactam was active against >75% of the Enterobacterales isolates from the ASPECT-NP trial that did not carry carbapenemases. K. pneumoniae strains resistant to ceftolozane-tazobactam might represent a challenge for treatment due to their multiple resistance mechanisms. Ceftolozane-tazobactam was among the agents that displayed the greatest activity against P. aeruginosa isolates. (This study has been registered at ClinicalTrials.gov under registration no. NCT02070757.).

Endophytic Lifestyle of Global Clones of Extended-Spectrum β-Lactamase-Producing Priority Pathogens in Fresh Vegetables: a Trojan Horse Strategy Favoring Human Colonization?

The global spread of antibiotic-resistant bacteria and their resistance genes is a critical issue that is no longer restricted to hospital settings, but also represents a growing problem involving environmental and food safety. In this study, we have performed a microbiological and genomic investigation of critical priority pathogens resistant to broad-spectrum cephalosporins and showing endophytic lifestyles in fresh vegetables sold in a country with high endemicity of extended-spectrum β-lactamases (ESBLs). We report the isolation of international high-risk clones of CTX-M-15-producing Escherichia coli, belonging to clonal complexes CC38 and CC648, and Klebsiella pneumoniae of complex CC307 from macerated tissue of surface-sterilized leaves of spinach, cabbage, arugula, and lettuce. Regardless of species, all ESBL-positive isolates were able to endophytically colonize common bean (Phaseolus vulgaris) seedlings, showed resistance to acid pH, and had a multidrug-resistant (MDR) profile to clinically relevant antibiotics (i.e., broad-spectrum cephalosporins, aminoglycosides, and fluoroquinolones). Genomic analysis of CTX-M-producing endophytic Enterobacterales revealed a wide resistome (antibiotics, biocides, disinfectants, and pesticides) and virulome, and genes for endophytic fitness and for withstanding acidic conditions. Transferable IncFIB and IncHI2A plasmids carried bla _CTX-M-15 genes and, additionally, an IncFIB plasmid (named pKP301cro) also harbored genes encoding resistance to heavy metals. These data support the hypothesis that fresh vegetables marketed for consumption can act as a figurative Trojan horse for the hidden spread of international clones of critical WHO priority pathogens producing ESBLs, and/or their resistance genes, to humans and other animals, which is a critical issue within a food safety and broader public and environmental health perspective.IMPORTANCE Extended-spectrum β-lactamases (ESBL)-producing Enterobacterales are a leading cause of human and animal infections, being classified as critical priority pathogens by the World Health Organization. Epidemiological studies have shown that spread of ESBL-producing bacteria is not a problem restricted to hospitals, but also represents a growing problem involving environmental and food safety. In this regard, CTX-M-type β-lactamases have become the most widely distributed and clinically relevant ESBLs worldwide. Here, we have investigated the occurrence and genomic features of ESBL-producing Enterobacterales in surface-sterilized fresh vegetables. We have uncovered that international high-risk clones of CTX-M-15-producing Escherichia coli and Klebsiella pneumoniae harboring a wide resistome and virulome, carry additional genes for endophytic fitness and resistance to acidic conditions. Furthermore, we have demonstrated that these CTX-M-15-positive isolates are able to endophytically colonize plant tissues. Therefore, we believe that fresh vegetables can act as a figurative Trojan horse for the hidden spread of critical priority pathogens exhibiting endophytic lifestyles.

Co-Production of NDM-1, CTX-M-9 Family and mcr-1 in a Klebsiella pneumoniae ST4564 Strain in China

Purpose

To identify novel sequence types 4564 (ST4564) carbapenem-resistant Klebsiella pneumoniae (CRKP). Characterizing the feature of the clinic, resistance, and virulence of a co-producing NDM-1 and CTX-M-9 family and mcr-1 ST4564 strain.

Methods

A novel ST4564 CRKP was collected from June 2018 to July 2018. We investigated its antimicrobial susceptibility by the microdilution method. Using the modified carbapenem inactivation method (mCIM) to screen phenotype of carbapenemases. Resistance mechanisms, virulence-associated genes, multilocus sequence typing (MLST), and capsular serotypes were characterized by polymerase chain reaction (PCR) and DNA sequencing. Next-generation sequencing (NGS) was carried out to determine the genetic features of carbapenem resistance and virulence.

Results

ST4564, co-carrying NDM-1, CTX-M-9 and mcr-1, was resistant to carbapenems, cephamycin, third- or fourth-generation cephalosporins, β-lactam combination agents, quinolones and tigecycline but remained susceptible to amikacin (AMK) and colistin (COL). Through the NGS analysis with the G+C content of 56.65%, multiple resistance and virulence genomes were detected. The genes encoding the β-lactams, aminoglycosides, quinolones, macrolides, sulfonamide, polysaccharide capsule, type-I fimbriae cluster, siderophore genes, transporter and pumps, T6SS and pullulanase secretion protein. goeBURST analysis showed that ST4564 belonged to the CC1571 and it was not related to the prevalent high-risk clones.

Conclusion

We first identified the novel ST4564 CRKP. Our finding suggested that the urgent need for infection control of the new clone to prevent it from becoming a high-risk clone of CRKP.

Susceptibility trends of ceftolozane/tazobactam and comparators when tested against U.S. gram-negative bacterial surveillance isolates (2012-2018)

Ceftolozane/tazobactam is an antipseudomonal cephalosporin combined with a β-lactamase inhibitor. Ceftolozane/tazobactam has been approved in >60 countries for treating complicated urinary tract infections, acute pyelonephritis, complicated intra-abdominal infections (with metronidazole), and hospital-acquired pneumonia, including ventilator-associated pneumonia in adults. We analyzed susceptibilities for 35,882 gram-negative isolates collected from patients in 35 US medical centers from 2012 to 2018. The rate of multi-drug resistant Enterobacterales was stable (9.5%-10.1%), while the P. aeruginosa multi-drug resistance rate increased from 15.5% in 2012 to 22.9% in 2018. The carbapenem-resistant Enterobacterales rates varied from 0.9% to 2.2% and extended-spectrum β-lactamase phenotypes increased from 10.5% to 16.8%. The most active drugs against P. aeruginosa were ceftolozane/tazobactam (95.8%-97.5% susceptible) and amikacin (93.9%-98.0%); against Enterobacterales, amikacin (97.9%-98.8%), meropenem (97.7%-98.8%), and ceftolozane/tazobactam (93.3%-95.6%) were the most active. These data suggest that ceftolozane/tazobactam has effective in vitro activity against organisms causing serious gram-negative infections.

In Vitro Activity Analysis of a New Polymyxin, SPR741, Tested in Combination with Antimicrobial Agents against a Challenge Set of Enterobacteriaceae, Including Molecularly Characterized Strains

The activities of azithromycin, fusidic acid, vancomycin, doxycycline, and minocycline were evaluated alone and in combination with SPR741. A total of 202 Escherichia coli and 221 Klebsiella pneumoniae isolates were selected, and they included a genome-sequenced subset (n = 267), which was screened in silico for β-lactamase, macrolide-lincosamide-streptogramin (MLS), and tetracycline (tet) genes. Azithromycin (>16 mg/liter), fusidic acid (>64 mg/liter), vancomycin (>16 mg/liter), and SPR741 (>8 mg/liter) showed off-scale MICs when each was tested alone against all isolates. MIC_50/90 results of 0.5/8 mg/liter, 4/>32 mg/liter, 16/>16 mg/liter, 2/32 mg/liter, and 0.25/4 mg/liter were obtained for azithromycin-SPR741, fusidic acid-SPR741, vancomycin-SPR741, doxycycline-SPR741 and minocycline-SPR741, respectively, against all isolates. Overall, azithromycin-SPR741 (MIC₉₀, 2 to 4 mg/liter) and minocycline-SPR741 (MIC₉₀, 0.5 to 2 mg/liter) showed the lowest MIC₉₀ values against different subsets of E. coli isolates, except for azithromycin-SPR741 (MIC₉₀, 16 mg/liter) against the AmpC and metallo-β-lactamase subsets. In general, minocycline-SPR741 (MIC₉₀, 2 to 8 mg/liter) had the lowest MIC₉₀ against K. pneumoniae isolates producing different groups of β-lactamases. The azithromycin-SPR741 MIC (MIC_50/90, 2/32 mg/liter) was affected by MLS genes (MIC_50/90 of 0.25/2 mg/liter against isolates without MLS genes), whereas doxycycline-SPR741 (MIC_50/90, 0.5/2 versus 8/32 mg/liter) and minocycline-SPR741 (MIC_50/90, 0.25/1 versus 1/8 mg/liter) MIC results were affected when tested against isolates carrying tet genes in general. However, minocycline-SPR741 inhibited 88.2 to 92.9% of tet-positive isolates regardless of the tet gene. The azithromycin-SPR741 MIC results (MIC_50/90, 1/16 mg/liter) against isolates with enzymatic MLS mechanisms were lower than against those with ribosomal protection (MIC_50/90, 16/>32 mg/liter). SPR741 increased the in vitro activity of tested codrugs at different levels and seemed to be dependent on the species and resistance mechanisms of the respective codrug.

Resistance among urinary tract pathogens collected in Europe during 2018

OBJECTIVES

Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis are urinary tract infection (UTI) pathogens and extended spectrum β-lactamase (ESBL)-producing pathogens exhibit co-resistance to oral fluoroquinolones (FQ) and trimethoprim-sulphamethoxazole (TMP-SMX). This study assessed the prevalence of ESBL phenotypes and co-resistance to FQ and TMP-SMX.

METHODS

In total, 766 E. coli, 260 K. pneumoniae and 104 P. mirabilis from UTIs in 18 countries were evaluated for susceptibility in the SENTRY surveillance programme, and results interpreted using EUCAST criteria.

RESULTS

E. coli, K. pneumoniae and P. mirabilis accounted for 57.1%, 11.3% and 7.8%, respectively, of the isolates. Among E. coli, resistance to levofloxacin and TMP-SMX ranged from 21.8% to 32.7% for all isolates increasing to 66.5-67.0% among those with a ESBL phenotype (17.9% of all UTI E. coli from Europe were ESBL phenotypes). In contrast, all E. coli were susceptible to meropenem. For K. pneumoniae, resistance rates for levofloxacin and TMP-SMX were 32.2-40.0% increasing to 69.1-78.6% for ESBL phenotypes. Meropenem was the most active agent, with 7.7% resistance. Among P. mirabilis resistance to levofloxacin and TMP-SMX was 26-38.5% and increased to 100% for ESBL phenotypes. No meropenem-resistant P. mirabilis were reported.

CONCLUSIONS

High co-resistance rates were observed for oral antibiotics among ESBL phenotypes raising concerns regarding empiric use of FQ and TMP-SMX for treating resistant UTIs outside of the hospital. In contrast, intravenous carbapenems retain activity against resistant UTI pathogens. New oral options with the spectrum of the carbapenems would address an unmet need for managing resistant UTIs.

International clones of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli in peri-urban wild animals, Brazil

CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli clones have been increasingly reported worldwide. In this regard, although discussions of transmission routes of these bacteria are in evidence, molecular data are lacking to elucidate the epidemiological impacts of ESBL producers in wild animals. In this study, we have screened 90 wild animals living in a surrounding area of São Paulo, the largest metropolitan city in South America, to monitor the presence of multidrug-resistant (MDR) Gram-negative bacteria. Using a genomic approach, we have analysed eight ceftriaxone-resistant E. coli. Resistome analyses revealed that all E. coli strains carried blaCTX-M -type genes, prevalent in human infections, besides other clinically relevant resistance genes to aminoglycosides, β-lactams, phenicols, tetracyclines, sulphonamides, trimethoprim, fosfomycin and quinolones. Additionally, E. coli strains belonged to international sequence types (STs) ST38, ST58, ST212, ST744, ST1158 and ST1251, and carried several virulence-associated genes. Our findings suggest spread and adaptation of international clones of CTX-M-producing E. coli beyond urban settings, including wildlife from shared environments.

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.

Omadacycline invitro activity against a molecularly characterized collection of clinical isolates with known acquired tetracycline resistance mechanisms

Omadacycline and tigecycline MIC₉₀ values were 2 μg/mL and 0.25 μg/mL, respectively, against Staphylococcus aureus carrying tet(M), whereas the minocycline, tetracycline, and doxycycline values were > 8 μg/mL. Similarly, omadacycline and tigecycline remained active against Enterococcus faecalis and Streptococcus pneumoniae harboring tet(L)and/or tet(M)(MIC₉₀, 0.06-0.25 μg/mL), whereas other tetracyclines were inactive (MIC₉₀, >8 μg/mL). Omadacycline and tigecycline remained more potent than minocycline, tetracycline, and doxycycline against Enterobacteriaceae carrying tet. This study demonstrates the effectiveness of modern tetracyclines, omadacycline, and tigecycline against isolates with tetracycline resistance genes.

Media for colistin susceptibility testing does not improve the detection of Klebsiella pneumoniae isolates carrying MgrB disruption and other mutation driven colistin resistance mechanisms

We evaluated different susceptibility testing media against 200 Klebsiella pneumoniae isolates that have been genetically characterized for the presence of polymyxin resistance mechanisms. The media evaluated included calcium enriched media that was described to promote separation of mcr-carrying Enterobacterales isolates and standard cation-adjusted Mueller-Hinton broth with and without polysorbate 80. The testing conditions evaluated did not show improvement in the separation of isolates carrying MgrB alterations and other mutation-driven polymyxin resistance mechanisms.

The burden of antimicrobial resistance among urinary tract isolates of Escherichia coli in the United States in 2017

Urinary tract infections (UTIs) caused by Escherichia coli have been historically managed with oral antibiotics including the cephalosporins, fluoroquinolones and trimethoprim-sulfamethoxazole. The use of these agents is being compromised by the increase in extended spectrum β-lactamase (ESBL)-producing organisms, mostly caused by the emergence and clonal expansion of E. coli multilocus sequence typing (ST) 131. In addition, ESBL isolates show co-resistance to many of oral agents. Management of UTIs caused by ESBL and fluoroquinolone-resistant organisms is becoming increasingly challenging to treat outside of the hospital setting with clinicians having to resort to intravenous agents. The aim of this study was to assess the prevalence of ESBL phenotypes and genotypes among UTI isolates of E. coli collected in the US during 2017 as well as the impact of co-resistance to oral agents such as the fluoroquinolones and trimethoprim-sulfamethoxazole. The national prevalence of ESBL phenotypes of E. coli was 15.7% and was geographically distributed across all nine Census regions. Levofloxacin and trimethoprim-sulfamethoxazole-resistance rates were ≥ 24% among all isolates and this co-resistance phenotype was considerably higher among isolates showing an ESBL phenotype (≥ 59.2%) and carrying bla_CTX-M-15 (≥ 69.5%). The agents with the highest potency against UTI isolates of E. coli, including ESBL isolates showing cross-resistance across oral agents, were the intravenous carbapenems. The results of this study indicate that new oral options with the spectrum and potency similar to the intravenous carbapenems would address a significant unmet need for the treatment of UTIs in an era of emergence and clonal expansion of ESBL isolates resistant to several classes of antimicrobial agents, including oral options.

Is it Time to Say Goodbye to Culture and Sensitivity? The Case for Culture-independent Urology

Next-generation sequencing has highlighted the limitations of conventional culture methods in the role of urology while discovering the intricate details of the role of microbiota in urologic health and disease. This review article explores: the utility and limitations of conventional culture methods; how culture-independent technologies are revolutionizing medicine; and how the implementation of these technologies may lead to improved patient outcomes. Finally, this article discusses the barriers to widespread adoption of culture-independent technologies, with suggestions for how these hurdles may be overcome.

Evaluation of Empiric β-Lactam Susceptibility Prediction among Enterobacteriaceae by Molecular β-Lactamase Gene Testing

The use of rapid diagnostic tests (RDTs) for blood cultures has become standard of care in the United States to inform early antimicrobial optimization. The relative ability of genotypic and phenotypic approaches to identify beta-lactam susceptibility in Escherichia coli, Klebsiella spp., and Proteus mirabilis was evaluated, using incidence rates of resistance mechanisms to third-generation cephalosporins, aztreonam, and piperacillin-tazobactam seen across U.S. census regions. Overall, the presence of CTX-M, KPC, and/or NDM genes was 81% (range, 57 to 87%) sensitive for the prediction of ceftriaxone, ceftazidime, and aztreonam resistance and 73% (range, 25 to 90%) sensitive for the detection of piperacillin-tazobactam resistance. The sensitivity of KPC or NDM to predict imipenem or meropenem resistance was 94.3% overall, and for meropenem ranged from 70 to 100% across U.S. census regions. Institutions that use genotypic RDTs to inform therapeutic de-escalation decisions should be aware of the incidence-base performance across U.S. geographies and in different patient populations, where resistance rates may vary.

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.