Analysis of the Correlation Between Antibiotic Resistance Patterns and Virulence Determinants in Pathogenic Klebsiella pneumoniae Isolates from Egypt

The Increased Prevalence of rmpA Gene in Klebsiella pneumoniae Isolates Coharboring blaNDM and blaOXA-48-like Genes

The emergence of carbapenemase-producing Klebsiella pneumoniae poses a substantial risk to public health. It is essential to comprehend the influence of carbapenemase on the virulence characteristics of K. pneumoniae in order to devise successful strategies for combating these infections. In this study, we explored the distribution disparity of virulence determinants between carbapenemase-producing (CP-Kp, n = 52) and carbapenemase-nonproducing (CN-Kp, n = 43) isolates. The presence of carbapenemases was detected via the modified carbapenem inactivation method and confirmed by PCR. The New Delhi metallo-β-lactamase (blaNDM) and Oxacillinase-48-like (blaOXA-48-like) genes were the most prevalent (94.23% and 76.92%, respectively) in CP-Kp isolates. Coexistence of blaNDM and blaOXA-48-like was observed in 71.15% of isolates, whereas 5.77% coharbored blaNDM and blaKPC. PCR analysis revealed the presence of several virulence genes, including adhesins (fimH, 92.63%, mrkD, 97.89%), capsule-associated virulence (uge, 90.53%), the K2 capsule serotype (k2, 6.32%), the iron acquisition system (kfu, 23.16%), and the regulator of mucoid phenotype (rmpA, 28.42%). A significantly higher prevalence of rmpA was detected in the CP-Kp compared with the CN-Kp (24/52 vs. 3/43, p < 0.0001), indicating a potential association between rmpA and carbapenemase acquisition. In addition, the majority of rmpA (22/24) positive isolates in the CP-Kp isolates coharbored blaNDM and either blaOXA-48-like or blaKPC.

Epidemiology, risk factors, and clinical outcomes of carbapenem-resistant Enterobacterales in Africa: A systematic review

OBJECTIVES

Carbapenem-resistant Enterobacterales (CRE) commonly cause hospital-acquired infections and hospital outbreaks worldwide, with an alarming increase in Africa, necessitating review of regional CRE epidemiological trends.

METHODS

A systematic review was conducted using PRISMA guidelines, searching PubMed, Scopus and Web of Science databases for studies describing CRE distribution, risk factors for CRE acquisition and clinical outcome of CRE infections in Africa.

RESULTS

One-hundred and sixty-nine studies were included, with the majority from North Africa (92/169, 54.4%). Most studies (136/169; 80.4%) focused only on infection, with a total of 15666 CRE isolates (97.4% clinical infection, 2.6% colonisation). The leading bacterial species included Klebsiella (72.2%), Escherichia coli (13.5%), and Enterobacter (8.3%). The most frequently detected carbapenemases were NDM (43.1%) and OXA-48-like (42.9%). Sequence types were reported in 44 studies, with ST101 and ST147 most commonly reported in K. pneumoniae, and ST410, ST167 and ST38 in E. coli. Previous antibiotic use, prior hospitalisation, surgical procedures, indwelling devices, intensive care unit admission and prolonged hospital stay, were the most frequent factors associated with CRE infection/colonisation. Crude mortality for CRE infection was 37%.

CONCLUSION

Although K. pneumoniae and E. coli remain the most frequent CRE in Africa, observed sequence types are not the commonly reported global 'high-risk' clones. The distribution of species and carbapenemases differs across African regions, while risk factors for CRE colonisation/infection, and patient outcomes are similar to those reported globally. There are limited data on CREs from parts of Africa, highlighting the need to strengthen epidemiologic surveillance programmes in the region.

Detection of Virulence Factors and Antibiotic Resistance among Klebsiella pneumoniae Isolates from Iran

The current study assessed the detection of virulence genes and drug resistance among Klebsiella pneumoniae isolates from Iran. During 2018 to 2020, 52 K. pneumoniae isolates were obtained from patients at Iran hospitals. By disk diffusion method, the antimicrobial susceptibility of K. pneumoniae isolates was assessed, and ESBL-producing K. pneumoniae isolates were detected by CDDT method. PCR analysis was done to detect virulence genes (iucB, iutA, iroN, kfu, allS, fimH, ybtS, mrkD, and entB); ESBL-encoding genes (bla TEM, bla PER, bla CTX-M, bla VEB, and bla SHV); and class D (bla OXA-48), class B (bla VIM, bla NDM, and bla IMP), and class A (bla KPC and bla GES) carbapenemase genes. Among all isolates, 84.6%, 13.5%, and 1.9% isolates were multidrug-resistant (MDR), extensively drug-resistant (XDR), and pandrug-resistant (PDR), respectively. Also, 84.6% were ESBL-producing and 71.2%, 53.8%, 40.4%, and 9.6% of all isolates were carrying bla TEM, bla SHV, bla CTX-M, and bla OXA-48 genes, respectively. Six isolates (11.5%) were positive for bla NDM gene. In contrast, no isolates were positive for the presence of bla KPC, bla IMP, and bla VIM. Virulence factor genes including iucB, iutA, iroN, kfu, allS, fimH, ybtS, mrkD, and entB were carried by 24%, 46.2%, 25%, 11.5%, 17.3%, 86.5%, 75%, 88.5%, and 100% isolates, respectively. This study evaluated the distribution and prevalence of virulence factor genes among K. pneumoniae isolates. The treatment of these infections is challenging due to the existence of particular virulence factors and the rise of antibiotic resistance. Therefore, the current study accentuates the necessity of finding new and efficient solutions for stopping the increase of antibiotic resistance.

Characteristics of Carbapenem-resistant Klebsiella pneumoniae in sewage from a tertiary hospital in Jilin Province, China

Carbapenem-resistant Klebsiella pneumoniae (CRKP) infection is a serious problem in hospitals worldwide. We monitored a tertiary hospital in Changchun, Jilin Province, China, and found that CRKP was the major species among the carbapenem-resistant isolates in sewage. Subsequently, we evaluated the drug susceptibility, resistance genes, virulence genes, outer pore membrane protein-related genes (OmpK35 & OmpK 36), multi-locus sequence typing and replicons, biofilm formation capabilities, and resistance to chlorine-containing disinfectants among KP isolates. Identification of drug sensitivity, multiple resistance profiles were observed including 77 (82.80%) multidrug resistant (MDR), 16 (17.20%) extensive drug resistant (XDR). Some antibiotic resistance genes were detected, the most prevalent carbapenemase gene was blaKPC, and 16 resistance genes were associated with other antibiotics. In addition, 3 (3.23%) CRKP isolates demonstrated loss of OmpK-35 and 2 (2.15%) demonstrated loss of OmpK-36. In the detection of multi-locus sequence typing (MLST), 11 ST11 isolates carried virulence genes. The most common replicon type was IncFII. Biofilm-forming capabilities were demonstrated by 68.8% of the isolates, all of which were resistant to chlorine-containing disinfectants. The results of the study showed that antibiotic-resistant isolates, especially CRKP, could resist disinfectants in hospital wastewater, and improper treatment of hospital wastewater may lead to the spread of drug-resistant bacteria and their genes. Thus, these bacteria must be eliminated before being discharged into the municipal sewage system.

Whole Genome Characterization of the High-Risk Clone ST383 Klebsiella pneumoniae with a Simultaneous Carriage of blaCTX-M-14 on IncL/M Plasmid and blaCTX-M-15 on Convergent IncHI1B/IncFIB Plasmid from Egypt

Recently, Egypt has witnessed the emergence of multidrug-resistant (MDR) Klebsiella pneumoniae, which has posed a serious healthcare challenge. The accelerated dissemination of bla_CTX-M genes among these MDR K. pneumoniae, particularly bla_CTX-M-14 and bla_CTX-M-15, have been noted. In this study, we investigated the occurrence of bla_CTX-M-IV among K. pneumoniae recovered from the laboratory of a major hospital in Alexandria. The 23 tested isolates showed an MDR phenotype and the bla_CTX-M-IV gene was detected in ≈22% of the isolates. The transformation of plasmids harboring bla_CTX-M-IV to chemically competent cells of Escherichia coli DH5α was successful in three out of five of the tested bla_CTX-M-IV-positive isolates. Whole genome sequencing of K22 indicated that the isolate belonged to the high-risk clone ST383, showing a simultaneous carriage of bla_CTX-M-14 on IncL/M plasmid, i.e., pEGY22_CTX-M-14, and bla_CTX-M-15 on a hybrid IncHI1B/IncFIB plasmid, pEGY22_CTX-M-15. Alignment of both plasmids revealed high similarity with those originating in the UK, Germany, Australia, Russia, China, Saudi Arabia, and Morocco. pEGY22_CTX-M-15 was a mosaic plasmid that demonstrated convergence of MDR and virulence genes. The emergence of such a plasmid with enhanced genetic plasticity constitutes the perfect path for the evolution of K. pneumoniae isolates causing invasive untreatable infections especially in a country with a high burden of infectious diseases such as Egypt. Therefore there is an imperative need for countrywide surveillances to monitor the prevalence of these superbugs with limited therapeutic options.

Multidrug-Resistant Klebsiella pneumoniae Causing Severe Infections in the Neuro-ICU

The purpose of this study was the identification of genetic lineages and antimicrobial resistance (AMR) and virulence genes in Klebsiella pneumoniae isolates associated with severe infections in the neuro-ICU. Susceptibility to antimicrobials was determined using the Vitek-2 instrument. AMR and virulence genes, sequence types (STs), and capsular types were identified by PCR. Whole-genome sequencing was conducted on the Illumina MiSeq platform. It was shown that K. pneumoniae isolates of ST14^K2, ST23^K57, ST39^K23, ST76^K23, ST86^K2, ST218^K57, ST219^KL125/114, ST268^K20, and ST2674^K47 caused severe systemic infections, including ST14^K2, ST39^K23, and ST268^K20 that were associated with fatal incomes. Moreover, eight isolates of ST395^K2 and ST307^{KL102/149/155} were associated with manifestations of vasculitis and microcirculation disorders. Another 12 K. pneumoniae isolates of ST395^K2,KL39, ST307^{KL102/149/155}, and ST147^K14/64 were collected from patients without severe systemic infections. Major isolates (n = 38) were XDR and MDR. Beta-lactamase genes were identified: bla_SHV (n = 41), bla_CTX-M (n = 28), bla_TEM (n = 21), bla_OXA-48 (n = 21), bla_NDM (n = 1), and bla_KPC (n = 1). The prevalent virulence genes were wabG (n = 41), fimH (n = 41), allS (n = 41), and uge (n = 34), and rarer, detected only in the genomes of the isolates causing severe systemic infections-rmpA (n = 8), kfu (n = 6), iroN (n = 5), and iroD (n = 5) indicating high potential of the isolates for hypervirulence.

Landscape of Multidrug-Resistant Gram-Negative Infections in Egypt: Survey and Literature Review

Purpose

This article is the first to review published reports on the prevalence of multidrug-resistant (MDR) gram-negative infections in Egypt and gain insights into antimicrobial resistance (AMR) surveillance and susceptibility testing capabilities of Egyptian medical centers.

Materials and Methods

A literature review and online survey were conducted.

Results

The online survey and literature review reported high prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (19–85.24% of E. coli, and 10–87% of K. pneumoniae), carbapenem-resistant Enterobacteriaceae (35–100% of K. pneumoniae and 13.8–100% of E. coli), carbapenem-resistant Acinetobacter baumannii (10–100%), and carbapenem-resistant Pseudomonas aeruginosa (15–70%) in Egypt. Risk factors for MDR Gram-negative infections were ventilated patients (67.4%), prolonged hospitalization (53.5%) and chronic disease (34.9%). Although antimicrobial surveillance capabilities were deemed at least moderate in most centers, lack of access to rapid AMR diagnostics, lack of use of local epidemiological data in treatment decision-making, lack of antimicrobial stewardship (AMS) programs, and lack of risk prediction tools were commonly reported by respondents.

Conclusion

This survey has highlighted the presence of knowledge gaps as well as limitations in the surveillance and monitoring capabilities of AMR in Egypt, with most laboratories lacking rapid diagnostics and molecular testing. Future efforts in Egypt should focus on tackling these issues via nationwide initiatives, including understanding the AMR trends in the country, capacity building of laboratories and their staff to correctly and timely identify AMR, and introducing newer antimicrobials for targeting emerging resistance mechanisms in Gram-negative species.