Dissemination and genetic support of broad-spectrum beta-lactam-resistant Escherichia coli strain isolated from two Tunisian hospitals during 2004-2012

Increased Incidence and Risk Factors of Infections by Extended-Spectrum β-Lactamase-Producing Enterobacterales During the COVID-19 Pandemic: A Retrospective Case-Control Study

Purpose

To investigate changes in the incidence of infections by extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) and analyzed whether there was an association between endogenous changes in the organism due to COVID-19 infection and the infections by ESBL-E.

Patients and Methods

The study was a single-center retrospective case-control design. A total of 107 patients infected by ESBL-E during the COVID-19 pandemic were selected as the case group, while 214 uninfected patients selected by 1:2 propensity score matching (PSM) acted as the control group. Univariate analysis, LASSO logistic regression, and multivariate logistic regression were used to determine the risk factors for ESBL-E infection. An interrupted time series was used to analyze the changes in the incidence of ESBL-E infections in hospitalized patients during the COVID-19 pandemic.

Results

The incidence of infection with ESBL-E showed a significant increase during COVID-19 (3.42 vs 4.92 per 1000 patients, p = 0.003). The incidence of ESBL-E infections increased at an average rate of 0.45 per 1000 patients per week compared to the pre-pandemic period (p = 0.022). Multivariate logistic regression analysis showed that a length of hospitalization ≥ 15 days (OR: 2.98 (1.07-8.28), chronic kidney disease (OR: 4.25 (1.32-13.70), white blood cell (WBC) > 9.5×10^9/L (OR: 3.04 (1.54-6.01), use of hormonal drugs (OR: 2.38 (1.04-5.43), antibacterial drug use 1 type (OR: 5.38 (2.04-14.21), antibacterial drug use 2 types (OR: 23.05 (6.71-79.25) and antibacterial drug use ≥ 3 types (OR: 88.35 (8.55-912.63) were independent risk factors for infection with ESBL-E, while chronic obstructive pulmonary disease (COPD) was a protective factor (OR: 0.14 (0.03-0.66). COVID-19 was not an independent risk factor for infection by ESBL-E.

Conclusion

During the COVID-19 pandemic, the incidence of infections by ESBL-E increased significantly. Increased exposure to traditional risk factors were the main reasons, however, COVID-19 was not an independent risk factor for ESBL-E infection.

Review and analysis of the overlapping threats of carbapenem and polymyxin resistant E. coli and Klebsiella in Africa

BACKGROUND

Carbapenem-resistant Enterobacterales are among the most serious antimicrobial resistance (AMR) threats. Emerging resistance to polymyxins raises the specter of untreatable infections. These resistant organisms have spread globally but, as indicated in WHO reports, the surveillance needed to identify and track them is insufficient, particularly in less resourced countries. This study employs comprehensive search strategies with data extraction, meta-analysis and mapping to help address gaps in the understanding of the risks of carbapenem and polymyxin resistance in the nations of Africa.

METHODS

Three comprehensive Boolean searches were constructed and utilized to query scientific and medical databases as well as grey literature sources through the end of 2019. Search results were screened to exclude irrelevant results and remaining studies were examined for relevant information regarding carbapenem and/or polymyxin(s) susceptibility and/or resistance amongst E. coli and Klebsiella isolates from humans. Such data and study characteristics were extracted and coded, and the resulting data was analyzed and geographically mapped.

RESULTS

Our analysis yielded 1341 reports documenting carbapenem resistance in 40 of 54 nations. Resistance among E. coli was estimated as high (> 5%) in 3, moderate (1-5%) in 8 and low (< 1%) in 14 nations with at least 100 representative isolates from 2010 to 2019, while present in 9 others with insufficient isolates to support estimates. Carbapenem resistance was generally higher among Klebsiella: high in 10 nations, moderate in 6, low in 6, and present in 11 with insufficient isolates for estimates. While much less information was available concerning polymyxins, we found 341 reports from 33 of 54 nations, documenting resistance in 23. Resistance among E. coli was high in 2 nations, moderate in 1 and low in 6, while present in 10 with insufficient isolates for estimates. Among Klebsiella, resistance was low in 8 nations and present in 8 with insufficient isolates for estimates. The most widespread associated genotypes were, for carbapenems, blaOXA-48, blaNDM-1 and blaOXA-181 and, for polymyxins, mcr-1, mgrB, and phoPQ/pmrAB. Overlapping carbapenem and polymyxin resistance was documented in 23 nations.

CONCLUSIONS

While numerous data gaps remain, these data show that significant carbapenem resistance is widespread in Africa and polymyxin resistance is also widely distributed, indicating the need to support robust AMR surveillance, antimicrobial stewardship and infection control in a manner that also addresses broader animal and environmental health dimensions.

Genetic Environments of Plasmid-Mediated blaCTXM-15 Beta-Lactamase Gene in Enterobacteriaceae from Africa

The most widely distributed blaCTX-M gene on a global scale is blaCTX-M-15. The dissemination has been associated with clonal spread and different types of mobile genetic elements. The objective of this review was to describe the genetic environments of the blaCTX-M-15 gene detected from Enterobacteriaceae in published literature from Africa. A literature search for relevant articles was performed through PubMed, AJOL, and Google Scholar electronic databases; 43 articles from 17 African countries were included in the review based on the eligibility criteria. Insertion sequences were reported as part of the genetic environment of blaCTX-M-15 gene in 32 studies, integrons in 13 studies, and plasmids in 23 studies. In this review, five insertion sequences including ISEcp1, IS26, orf447, IS903, and IS3 have been detected which are associated with the genetic environment of blaCTX-M-15 in Africa. Seven different genetic patterns were seen in the blaCTX-M-15 genetic environment. Insertion sequence ISEcp1 was commonly located upstream of the end of the blaCTX-M-15 gene, while the insertion sequence orf477 was located downstream. In some studies, ISEcp1 was truncated upstream of blaCTX-M-15 by insertion sequences IS26 and IS3. The class 1 integron (Intl1) was most commonly reported to be associated with blaCTX-M-15 (13 studies), with Intl1/dfrA17–aadA5 being the most common gene cassette array. IncFIA-FIB-FII multi-replicons and IncHI2 replicon types were the most common plasmid replicon types that horizontally transferred the blaCTX-M-15 gene. Aminoglycoside-modifying enzymes, and plasmid-mediated quinolone resistance genes were commonly collocated with the blaCTX-M-15 gene on plasmids. This review revealed the predominant role of ISEcp1, Intl1 and IncF plasmids in the mobilization and continental dissemination of the blaCTX-M-15 gene in Africa.

Screening for Carbapenemases in Ertapenem-Resistant Enterobacteriaceae Collected at a Tunisian Hospital Between 2014 and 2018

Background

Carbapenem-resistance is frequently detected in Enterobacteriaceae isolated from patients in Tunisia. The study was performed to identify frequent carbapenemases in Tunisian isolates.

Methods

Between May 2014 and January 2018, 197 ertapenem-resistant Enterobacteriaceae were isolated at the microbiological department of the Military Hospital of Tunis. The strains were phenotypically characterized and then subjected to in-house polymerase chain reaction (PCR) targeting the carbapenemase genes bla_IMP, bla_VIM, bla_NDM, bla_SPM, bla_AIM, bla_DIM,bla_GIM, bla_SIM, bla_KPC, bla_BIC, and bla_OXA-48.

Results

The assessed 197 ertapenem-resistant Enterobacteriaceae from Tunis comprised 170 Klebsiella pneumoniae, 19 Enterobacter cloacae, 6 Escherichia coli, 1 Citrobacter sedlakii, and 1 Enterobacter asburiae. Thereby, 55 out of 197 isolates (27.9%) were from blood cultures, suggesting a systemic disease. The carbapenemase gene bla_OXA-48 quantitatively dominated by far with 153 detections, followed by bla_NDM with 14 detections, which were distributed about the whole study interval. In contrast, bla_BIC and bla_VIM were only infrequently identified in 5 and 3 cases, respectively, while the other carbapenamases were not observed.

Conclusions

The carbapenemase gene bla_OXA-48 was identified in the vast majority of ertapenem-resistant Tunisian Enterobacteriaceae while all other assessed carbapenemases were much less abundant. In a quantitatively relevant minority of isolates, the applied PCR-based screening approach did not identify any carbapenemases.

Prevalence of extended-spectrum β-lactamase-producing Klebsiella pneumoniae: First systematic review and meta-analysis from Iran

OBJECTIVES

Extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-KP) have emerged as an important pathogen causing severe infections worldwide. Infections due to ESBL-KP are associated with high morbidity and mortality, especially in developing countries such as Iran. The aim of this study was to assess the pooled prevalence of ESBL-KP with different gene variants in Iran.

METHODS

A literature search of Medline (via PubMed), Embase, Web of Science and Iranian Database was performed. A meta-analysis was conducted using Comprehensive Meta-Analysis Software (version 2.2, Biostat). A fixed- or random-effects model was used based on the heterogeneity test. Publication bias was determined using Begg's rank correlation and Egger's weighted regression methods.

RESULTS

Among 783 articles identified, 43 studies met the eligibility criteria. The pooled prevalence of ESBL-KP was 43.5% (95% CI 39.3-47.9%) among clinical K. pneumoniae isolates. Among genes encoding ESBLs during 2000-2009, SHV, CTX-M and TEM were found with prevalences of 23.3%, 15.2% and 12.3%, respectively, whilst the prevalences of SHV, CTX-M, TEM and VEB were 24%, 28.1%, 25.2% and 8.3%, respectively, during the period 2010-2018.

CONCLUSION

The prevalence of ESBL-KP has increased steadily in recent years among clinical K. pneumoniae isolates in Iran. Thus, initial identification of ESBL-KP according to Clinical and Laboratory Standards Institute (CLSI) guidelines, proper molecular approaches, and implementation of antimicrobial stewardship programmes in Iranian hospitals together with comprehensive infection control measures are urgently needed to control the dissemination of these strains.