Outcomes and Risk Factors for Mortality among Patients Treated with Carbapenems for Klebsiella spp. Bacteremia

Whole-genome sequencing of clinical isolates of Klebsiella michiganensi in China carrying blaIPM-4 and blaNDM-1

AIM

This study aimed to analyze the prevalence, phenotypes, and carriage of resistance genes of carbapenem-resistant Klebsiella michiganensis strains isolated in our hospital.

METHOD

ology: Four K. michiganensis strains were collected from January 2015 to December 2023. Antimicrobial susceptibility was tested using 21 antibiotics with the BD Phoenix™ M50 System. Whole-genome sequencing of the four strains was performed on an Illumina NovaSeq 6000 platform. Species identification was performed using Kleborate software, sequence type (ST) was performed using MLST, and prediction of antibiotic resistance genes and virulence genes were performed using ABRicate. PlasmidFinder was used to search for plasmids. Whole genome data from 211 strains of carbapenem-resistant K. michiganensis were downloaded from the NCBI database; together with the strains in this study, these data were used to construct an phylogenetic tree using genome single nucleotide polymorphisms (SNP).

RESULTS

Antimicrobial susceptibility showed that K. michiganensis was highly resistant to β-lactams. For the three carbapenems, strain WF0046 was only resistant to ertapenem, while WF0047, WF0052, and WF0053 were resistant to all three carbapenems tested. The four strains of K. michiganensis only showed complete sensitivity to polymyxin E and tigecycline. The four K. michiganensis strains were found to have 43 resistance genes, and all carried carbapenem resistance genes; WF0046 carried the carbapenem resistance gene blaIMP-4, while the other three strains carried blaNDM-1. Among the other resistance genes, β-lactam resistance genes were predicted most (11 types), followed by eight types of aminoglycoside resistance genes. Of the strains characterized in this study, WF0046 belonged to ST158, WF0047 belonged to ST40, WF0052 belonged to ST533, and WF0053 belonged to ST13. These four strains, along with 211 carbapenem-resistant K. michiganensis strains downloaded from NCBI, were divided into five clades; WF0052 belonged to clade A, WF0046 belonged to clade C, and WF0047 and WF0053 both belonged to clade D. The four strains had relatively distant genetic relationships; WF0046, WF0047, and WF0053 were closely related to strains of human origin from other regions of China, while WF0052 was genetically close with a strain of K. michiganensis isolated in the United States.

CONCLUSION

The strains of K. michiganensis from our hospital were resistant to multiple antibiotics, and all strains carried carbapenem resistance genes along with multiple other antibiotic resistance genes. The phylogenetic results showed that these four strains had distant genetic relationships and different ST types, indicating that they came from different sources and the possibility of polyclonal transmission.

The Practical Problem With Carbapenem Testing and Reporting Accurate Bacterial Susceptibilities

Background: Antibiotic resistance is an evolving issue which requires constant review. Susceptibility breakpoints are revised in line with new microbiological and pharmacological data. Susceptibility breakpoints for carbapenems and Enterobacterales were revised in response to the rise in resistance and the potential for standard doses of carbapenems to provide the necessary antibiotic exposure and to accurately identify rates of carbapenem resistance.

Objectives: This review sought to identify real-world implications associated with lack of testing and reporting current carbapenem breakpoints and potential barriers that may impede implementation of these strategies.

Methods: A literature review was conducted using PubMed and Google Scholar electronic databases.

Results: The failure to adopt revised breakpoints incurs negative clinical outcomes and carries increased cost implications. However, there were several impediments highlighted which are barriers for laboratories to implement breakpoint updates.

Conclusion: Possible practical steps to implement revised breakpoints which apply to carbapenems and Enterobacterales are proposed. The challenge for laboratories is to be aware and implement these changes to provide accurate and relevant susceptibility results for clinicians.

Attributable burden in patients with carbapenem-nonsusceptible gram-negative respiratory infections

Objective

We aimed to describe the clinical and economic burden attributable to carbapenem-nonsusceptible (C-NS) respiratory infections.

Methods

This retrospective matched cohort study assessed clinical and economic outcomes of adult patients (aged ≥18 years) who were admitted to one of 78 acute care hospitals in the United States with nonduplicate C-NS and carbapenem-susceptible (C-S) isolates from a respiratory source. A subset analysis of patients with principal diagnosis codes denoting bacterial pneumonia or other diagnoses was also conducted. Isolates were classified as community- or hospital-onset based on collection time. A generalized linear mixed model method was used to estimate the attributable burden for mortality, 30-day readmission, length of stay (LOS), cost, and net gain/loss (payment minus cost) using propensity score-matched C-NS versus C-S cohorts.

Results

For C-NS cases, mortality (25.7%), LOS (29.4 days), and costs ($81,574) were highest in the other principal diagnosis, hospital-onset subgroup; readmissions (19.4%) and net loss (-$9522) were greatest in the bacterial pneumonia, hospital-onset subgroup. Mortality and readmissions were not significantly higher for C-NS cases in any propensity score-matched subgroup. Significant C-NS–attributable burden was found for both other principal diagnosis subgroups for LOS (hospital-onset: 3.7 days, P = 0.006; community-onset: 1.5 days, P<0.001) and cost (hospital-onset: $12,777, P<0.01; community-onset: $2681, P<0.001).

Conclusions

Increased LOS and cost burden were observed in propensity score-matched patients with C-NS compared with C-S respiratory infections; the C-NS–attributable burden was significant only for patients with other principal diagnoses.

Assessment of mortality stratified by meropenem minimum inhibitory concentration in patients with Enterobacteriaceae bacteraemia: A patient-level analysis of published data

In 2010, the Clinical and Laboratory Standards Institute (CLSI) lowered carbapenem breakpoints to reduce the proportion of 'susceptible' organisms that produced carbapenemases. Few studies have evaluated the effect of this change on clinical outcomes. This systematic review aimed to evaluate the effect of carbapenem MICs on 30-day mortality from pooled patient-level data from studies of patients treated with carbapenems across a range of meropenem MICs. PubMed was searched to March 2019 with the terms 'carbapenem', 'meropenem', 'imipenem', 'doripenem', 'ertapenem', 'susceptibility' and 'outcomes'. Studies were included in the analysis if patients had Enterobacteriaceae bacteraemia treated with a carbapenem for ≥48 h and mortality was reported. Studies were excluded if all isolates were either susceptible or resistant to meropenem based on CLSI 2010 breakpoints or if only carbapenemase-producing isolates were included. Authors were contacted for patient-level data. The primary outcome was 30-day mortality, with planned subset analyses of patients treated with meropenem, receiving active combination therapy, treated in the ICU or infected with Klebsiella pneumoniae. Of 157 articles identified, 4 met the inclusion criteria (115 eligible patients). The odds of mortality increased with each increasing meropenem MIC dilution (OR = 1.51, 95% CI 1.06-2.15) as a continuous variable. A similar increase in odds was observed in patients treated with meropenem, treated in the ICU, infected with K. pneumoniae or receiving no other active antimicrobials. Increasing meropenem MICs in Enterobacteriaceae were associated with increased mortality; however, more work is needed to define optimal clinical decision rules for infections within the susceptible range.

Association between carbapenem-resistant Enterobacteriaceae and death: A systematic review and meta-analysis

BACKGROUND

Carbapenem-resistant Enterobacteriaceae (CRE) has emerged in health care facilities around the world. Several studies demonstrated data regarding clinical outcomes for CRE infections including death. This systematic review and meta-analysis summarized literature discussing association between CRE and mortality.

METHODS

A systematic literature review was performed by searching EMBASE, International Pharmaceutical Abstract databases, PubMed, and Scopus and to identify studies that assessed the association between CRE and death published from April 2012 to October 2017. A meta-analysis was performed using a random effect model. Heterogeneity was assessed using the I²-statistic.

RESULTS

Twenty-one studies were included in this meta-analysis. The underlying populations were moderately heterogeneous (I² = 60%; P = .01). Pooled risk estimates from 9 studies revealed a significant association between CRE and death (pooled-adjusted odds ratio: 2.85; 95% confidence interval: 1.88, 4.30). The unadjusted variable pooled from 18 studies demonstrated a significant association between CRE and death (pooled-unadjusted odds ratio: 3.73; 95% confidence interval: 2.02, 6.88).

DISCUSSION

The finding that CRE infection was positively associated with death agreed with the previous meta-analysis of studies published before April 2012.

CONCLUSIONS

This meta-analysis found that CRE was associated with increased risk of death. Our analysis implies a need for strict infection control measures.

Attributable clinical and economic burden of carbapenem-non-susceptible Gram-negative infections in patients hospitalized with complicated urinary tract infections

BACKGROUND

Gram-negative complicated urinary tract infections (cUTIs) can have serious consequences for patients and hospitals.

AIM

To examine the clinical and economic burden attributable to Gram-negative carbapenem-non-susceptible (C-NS; resistant/intermediate) infections compared with carbapenem-susceptible (C-S) infections in 78 US hospitals.

METHODS

All non-duplicate C-NS and C-S urine source isolates were analysed. A subset had principal diagnosis ICD-9-CM codes denoting cUTI. Collection time (<3 vs ≥3 days after admission) determined isolate classification as community or hospital onset. Mortality, 30-day re-admissions, length of stay (LOS), hospital cost and net gain/loss in US dollars were determined for C-NS and C-S cases, with the C-NS-attributable burden estimated through propensity score matching. Three subgroups with adequate patient numbers were analysed: cUTI principal diagnosis, community onset; other principal diagnosis, community onset; and other principal diagnosis, hospital onset.

FINDINGS

The C-NS-attributable mortality risk was significantly higher (58%) for the other principal diagnosis, hospital-onset subgroup alone (odds ratio 1.58, 95% confidence interval 1.14-2.20; P < 0.01). The C-NS-attributable risk for 30-day re-admission ranged from 29% to 55% (all P < 0.05). The average attributable economic impact of C-NS was 1.1-3.9 additional days LOS (all P < 0.05), US$1512-10,403 additional total cost (all P < 0.001) and US$1582-11,848 net loss (all P < 0.01); overall burden and C-NS-attributable burden were greatest in the other principal diagnosis, hospital-onset subgroup.

CONCLUSION

Greater clinical and economic burden was observed in propensity-score-matched patients with C-NS infections compared with C-S infections, regardless of whether cUTI was the principal diagnosis, and this burden was most severe in hospital-onset infections.

Estimating the burden of antimicrobial resistance: a systematic literature review

Background

Accurate estimates of the burden of antimicrobial resistance (AMR) are needed to establish the magnitude of this global threat in terms of both health and cost, and to paramaterise cost-effectiveness evaluations of interventions aiming to tackle the problem. This review aimed to establish the alternative methodologies used in estimating AMR burden in order to appraise the current evidence base.

Methods

MEDLINE, EMBASE, Scopus, EconLit, PubMed and grey literature were searched. English language studies evaluating the impact of AMR (from any microbe) on patient, payer/provider and economic burden published between January 2013 and December 2015 were included. Independent screening of title/abstracts followed by full texts was performed using pre-specified criteria. A study quality score (from zero to one) was derived using Newcastle-Ottawa and Philips checklists. Extracted study data were used to compare study method and resulting burden estimate, according to perspective. Monetary costs were converted into 2013 USD.

Results

Out of 5187 unique retrievals, 214 studies were included. One hundred eighty-seven studies estimated patient health, 75 studies estimated payer/provider and 11 studies estimated economic burden. 64% of included studies were single centre. The majority of studies estimating patient or provider/payer burden used regression techniques. 48% of studies estimating mortality burden found a significant impact from resistance, excess healthcare system costs ranged from non-significance to $1 billion per year, whilst economic burden ranged from $21,832 per case to over $3 trillion in GDP loss. Median quality scores (interquartile range) for patient, payer/provider and economic burden studies were 0.67 (0.56-0.67), 0.56 (0.46-0.67) and 0.53 (0.44-0.60) respectively.

Conclusions

This study highlights what methodological assumptions and biases can occur dependent on chosen outcome and perspective. Currently, there is considerable variability in burden estimates, which can lead in-turn to inaccurate intervention evaluations and poor policy/investment decisions. Future research should utilise the recommendations presented in this review.

Trial registration

This systematic review is registered with PROSPERO (PROSPERO CRD42016037510).

Characterization and formulation into solid dosage forms of a novel bacteriophage lytic against Klebsiella oxytoca

AIM

To isolate and characterize bacteriophage lytic for the opportunistic pathogen Klebsiella oxytoca and their formulation into a range of solid dosage forms for in-vitro testing.

METHODS AND RESULTS

We report the isolation, genomic and functional characterization of a novel bacteriophage lytic for Klebsiella oxytoca, which does not infect the closely related Klebsiella pneumoniae. This bacteriophage was formulated into suppositories and troches and shown to be released and lyse underlying Klebsiella oxytoca bacteria in an in-vitro model. These bacteriophage formulations were stable for at least 49 days at 4°C.

CONCLUSIONS

The successful in-vitro assay of these formulations here suggests that they could potentially be tested in-vivo to determine whether such a therapeutic approach could modulate the gut microbiome, and control Klebsiella oxytoca overgrowth, during antibiotic therapy regimes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study reports a novel bacteriophage specific for Klebsiella oxytoca which can be formulated into solid dosage forms appropriate for potential delivery in testing as a therapy to modulate gut microbiome during antibiotic therapies.

A new assay for the simultaneous identification and differentiation of Klebsiella oxytoca strains

Klebsiella oxytoca is the second most frequently identified species of Klebsiella isolated from hospitalized patients. Klebsiella spp. is difficult to identify using conventional methods and is often misclassified in clinical microbiology laboratories. K. oxytoca is responsible for an increasing number of multi-resistant infections in hospitals because of insufficient detection and identification. In this study, we propose a new simple method called pehX-LM PCR/XbaI, which simultaneously indicates K. oxytoca species and genotype by the fingerprint pattern. The pehX-LM PCR/XbaI is a combination of the following two methods: species-specific amplification of pehX gene and non-specific amplification of short restriction fragments by the LM PCR method. The specificity and the discrimination power of the pehX-LM PCR/XbaI method were determined by typing 209 K. oxytoca strains (included 9 reference strains), 28 K. pneumoniae, and other 25 strains belonging to the Enterobacteriaceae. The typing results were confirmed by the PCR melting profile method. Unlike the known fingerprinting methods, the pehX-LM PCR/XbaI leads to a clear pattern (approx. 3–5 bands) with a sufficient, relatively high discriminatory power. As a result, the time and cost of a single analysis are lower. The method can be used both in clinical and environmental research.

High minimum inhibitory concentration of imipenem as a predictor of fatal outcome in patients with carbapenem non-susceptible Klebsiella pneumoniae

Carbapenem resistance in Klebsiella pneumoniae is important because of its increasing prevalence and limited therapeutic options. To investigate the clinical and microbiological characteristics of patients infected or colonized with carbapenem non-susceptible K. pneumoniae (CnsKP) in Taiwan, we conducted a retrospective study at Taipei Veterans General Hospital from January 2012 to November 2013. Carbapenem non-susceptibility was defined as a minimum inhibitory concentration (MIC) of ≥2 mg/L for imipenem or meropenem. A total of 105 cases with CnsKP were identified: 49 patients with infection and 56 patients with colonization. Thirty-one isolates had genes that encoded carbapenemases (29.5%), including K. pneumoniae carbapenemase (KPC)-2 (n = 27), KPC-3 (n = 1), VIM-1 (n = 1) and IMP-8 (n = 2). The in-hospital mortality among patients with CnsKP was 43.8%. A MIC for imipenem ≥16 μg/mL, nasogastric intubation and Acute Physiology and Chronic Health Evaluation II score were independent risk factors for in-hospital mortality for all patients with CnsKP. A MIC for imipenem ≥16 μg/mL was also an independent risk factor for 14-day mortality in patients with CnsKP. In conclusion, a positive culture for CnsKP was associated with high in-hospital mortality. A high imipenem MIC of CnsKP can predispose a patient to a poor prognosis.

Complete Nucleotide Sequence of IncP-1β Plasmid pDTC28 Reveals a Non-Functional Variant of the blaGES-Type Gene

Plasmid pDTC28 was isolated from the sediments of Haihe River using E. coli CV601 (gfp-tagged) as recipient and indigenous bacteria from the sediment as donors. This plasmid confers reduced susceptibility to tetracycline and sulfamethoxazole. The complete sequence of plasmid pDTC28 was 61,503 bp in length with an average G+C content of 64.09%. Plasmid pDTC28 belongs to the IncP-1β group by phylogenetic analysis. The backbones of plasmid pDTC28 and other IncP-1β plasmids are very classical and conserved, whereas the accessory regions of these plasmids are diverse. A bla_GES-5-like gene was found on the accessory region, and this bla_GES-5-like gene contained 18 silent mutations and 7 missense mutations compared with the bla_GES-5 gene. The mutations resulted in 7 amino acid substitutions in GES-5 carbapenemase, causing the loss of function of the bla_GES-5-like gene on plasmid pDTC28 against carbapenems and even β-lactams. The enzyme produced by the bla_GES-5-like gene cassette may be a new variant of GES-type enzymes. Thus, the plasmid sequenced in this study will expand our understanding of GES-type β-lactamases and provide insights into the genetic platforms used for the dissemination of GES-type genes.

What tuberculosis can teach us about combating multidrug-resistant Gram negative bacilli

There are striking similarities between the dual pandemics of multidrug-resistant tuberculosis (MDR TB) and multidrug-resistant Gram negative bacilli (MDR GNB) despite fundamental differences in the pathogenesis and epidemiology of these pathogens. In this perspective, we highlight several strategies that have been used by the global TB community to address the MDR TB problem, including approaches to: encourage appropriate use of anti-TB medications, enhance appropriate utilization of molecular diagnostic testing, facilitate development of new antimicrobial agents, and strengthen surveillance systems and infection control practices. Understanding the successes and challenges of these strategies for MDR TB control will be instructive for efforts to curb emergence and spread of MDR GNB.