Whole-genome sequencing of Egyptian multidrug-resistant Klebsiella pneumoniae isolates: a multi-center pilot study

Multidrug-resistant (MDR) Klebsiella pneumoniae is a common infectious pathogen. We performed whole-genome sequencing (WGS) of 39 randomly selected, geographically diverse MDR K. pneumoniae from nine Egyptian hospitals. Clinical sources, phenotypic antibiotic resistance, and hyper-mucoviscosity were documented. WGS data were epidemiologically interpreted and tested for the presence of antibiotic resistance and virulence genes. Based on WGS data, we identified 18 classical multi-locus sequence types (MLST), the most common type being ST101 (23.1%) followed by ST147 (17.9%). Phylogenetic analyses identified small numbers of closely related isolates in a few of the centers, so we mostly documented independent nosocomial acquisition or import from public sources. The most common acquired resistance gene found was bla_CTX-M-15, detected in 27 isolates (69.2%). Carbapenemase genes encountered were bla_NDM-1 (n = 13), bla_NDM-5 (n = 1), bla_OXA-48 (n = 12), bla_OXA-181 (n = 2), and bla_KPC2 (n = 1). Seven strains (18%) contained more than a single carbapenemase gene. While searching for virulence-associated genes, sixteen wzi alleles were identified with wzi137, wzi64, and wzi50 most commonly found in ST101, ST147, and ST16, respectively. Yersiniabactin was the most common virulence factor (69.2%). Hyper-mucoviscosity was documented for 6 out of 39 isolates.This is the first genomic study of MDR K. pneumoniae from Egypt. The study revealed a clear spread of well-known international clones and their associated antimicrobial resistance and (hyper)virulence traits. The clinical situation in Egypt seems to reflect the scenario documented in many other countries and requires close attention.

Molecular Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolated from Egyptian Pediatric Cancer Patients Including a Strain with a Rare Gene-Combination of β-Lactamases

PURPOSE

Healthcare-associated infections caused by multi-drug-resistant (MDR) pathogens are a global threat. We aim to assess the clonal relatedness among carbapenemase-producing Klebsiella pneumoniae (CPKP) strains infecting Egyptian pediatric cancer patients.

MATERIALS AND METHODS

Identification and antimicrobial susceptibility testing of 149 Gram-negative isolates obtained from pediatric cancer patients were performed by VITEK 2. Genes encoding carbapenemases and extended-spectrum β-lactamases were detected by PCR and verified by DNA sequencing of representative samples. The transferability of the plasmids harboring bla OXA-48, from representative clinical samples, was evaluated by performing a conjugation experiment followed by PCR and MIC shift determination. Clonal relationships among the bla OXA-48-harboring K. pneumoniae isolates were determined by enterobacterial repetitive intergenic consensus (ERIC)-PCR and pulsed-field gel electrophoresis (PFGE).

RESULTS

Carbapenem resistance was observed in 59% of the isolates. The most prevalent species was K. pneumoniae (45.6%) and 57% of them were isolated from ICU. Fifty-nine % of the K. pneumoniae isolates were carbapenemase-producers and bla OXA-48 was detected in (58%) of them. One isolate co-harbored bla OXA-48, bla NDM-1, and bla IMP-1 genes for the first time in Egypt. PCR and meropenem MIC shift confirmed the success of the transferability of representative plasmids to E. coli K12. ERIC and PFGE identified 93% and 100% of the K. pneumoniae with a similarity coefficient ≥85%, respectively, including strains with indistinguishable patterns, suggesting possible clonal dissemination.

CONCLUSION

Our findings underline the dissemination of diverse clones of MDR CPKP among Egyptian pediatric cancer patients. Hence, routine molecular characterizations followed by strict implementation of infection control measures are crucial to tackling this threat.

The TACTIC experience: establishing an international, interdisciplinary network to tackle antimicrobial resistance

Antimicrobial resistance (AMR) is a major global health threat that requires an interdisciplinary international approach to address. In response to calls from policymakers and funders alike, a growing number of research networks on AMR have been created with this approach in mind. However, there are many challenges facing researchers in establishing such networks and research projects. In this article, we share our experience of establishing the network 'TACTIC: Tackling AMR Challenges through Translational Interdisciplinary Collaborations'. Although presented with many challenges both scientific and logistical, the network has underpinned productive interaction between biomedical and social scientists from several countries and fostered true collaboration in an educative, stimulating and sustainable way that forms a platform for important research on AMR.

Multiple sequence types responsible for healthcare-associated Acinetobacter baumannii dissemination in a single centre in Egypt

Background

Acinetobacter baumannii is an increasingly worrying organism in the healthcare setting, due to its multidrug resistance and persistence. Prolonged hospitalisation, immunocompromised patients and excessive antibiotic exposure all contribute to increasing the risk of A. baumannii infections, which makes cancer patients a significant risk group. This study aims to investigate the dissemination of A. baumannii at the National Cancer Institute (NCI) in Cairo – Egypt.

Methods

All bacterial isolates were typed using Multi-locus Sequence Typing (MLST) to characterise the epidemiology of isolates. The intrinsic OXA-51-like, and the acquired carbapanemases OXA-23, − 24/40, − 58, NDM, IMP, and VIM were also amplified and sequenced to genetically identify mechanisms of carbapenem resistance.

Results

MLST results show a high degree of multi-clonal dissemination, with 18 different Sequence Types (STs) identified, including 5 novel. The majority of isolates belonged to International Clone (IC) 2, and carbapenem resistance was detected in 93% of isolates and mediated by bla_OXA-23, bla_OXA-58, bla_NDM-1 and bla_VIM-1. We also report the presence of a resistant ST732 (OXA-378) which has been previously identified in migratory birds_.

Conclusions

Multiple highly resistant clones were identified in a Cancer hospital in Cairo. It is vital that clinicians and healthcare workers are aware of the population of A. baumannii present in order to have appropriate treatment and infection control practices.

Overview and outcome of mucormycosis among children with cancer: Report from the Children's Cancer Hospital Egypt

Mucormycosis represents a real challenge in immunocompromised patients. This study aimed to describe the clinical characteristics, treatment outcome and infection-related mortality in our patients at the Children's Cancer Hospital 57357, Cairo, Egypt. This is a retrospective study during the period 2007-2017. Data analysis included demographic data, risk factors, diagnostic workup, treatment and outcome. During the study period, 45 patients developed proven mucormycosis according to EORTC/MSG criteria (2008). Ninety percentof cases were of haematological malignancies. Liposomal amphotericin B was the mainstay of treatment. Posaconazole was used as secondary prophylaxis in 35% of cases. Combination antifungal was used in three cases with progressive mucormycosis. Surgical intervention was achievable in 50% of cases. Therapy was successful in 35 patients (66%). Complications related to mucormycosis were seen in five cases with disfigurement and perforated hard palate. Chemotherapy delay with subsequent relapse of primary malignancy was reported in one case. Mucormycosis-related mortality was 33% (15 cases). Mucormycosis is a major cause of mortality among patients with haematological malignancies. Early diagnosis of Mucormycosis infection, with rapid initiation of appropriate antifungal therapy and surgical intervention, whenever feasible, is the backbone of mucormycosis treatment.

Source, pattern and antibiotic resistance of blood stream infections in hematopoietic stem cell transplant recipients

Mucositis developing as a result of myelo-ablative high dose therapy administered prior to hematopoietic stem cell transplantation (HSCT) is associated with the risk of bacteremia. The aim of the present study was to detect the pattern of bacteremia coinciding with the present practice of HSCT, to study the contribution of health-care associated infection (HAI) to the pattern of infection, in the context of the problem of antibiotic resistance in HSCT recipients.

PATIENTS AND METHODS

This is a retrospective, single center study including patients who developed febrile neutropenia (FN) among HSCT recipients in one year duration.

RESULTS

Ninety FN episodes were recorded in 50 patients. Out of 39 positive blood cultures, Gram negative rods (GNR) were the predominant pathogens, constituting 67% (n=26) of isolated organisms, while 33% of infections were caused by gram positive cocci (GPC) (n=13). Bacteremia was significantly associated with central venous line (CVL) infections and gastroenteritis (diarrhea and vomiting) with a p-value 0.024, 0.20 and 0.0001, respectively. Multi-drug resistant organisms (MDROs) were identified in 27 (69%) of the 39 positive blood cultures.

CONCLUSION

In one year duration, gram negative pathogens were the predominant causes of infection in HSCT recipients with high rates of MDROs in our institution. Gastroenteritis and central venous line infections are the main sources of bacteremia.

Clinical and microbiologic determinants of serious bloodstream infections in Egyptian pediatric cancer patients: a one-year study

OBJECTIVES

Bloodstream infections (BSI) remain a major cause of morbidity and death in patients undergoing treatment for cancer. However, all recent epidemiological and therapeutic studies underline the absolute need for knowledge of the factors governing the infections in each center. The aim of this study is to identify the factors affecting BSI in the pediatric service of the National Cancer Institute (NCI) at Cairo University. More tailored policies for the treatment of patients with febrile neutropenia following chemotherapy can then be created.

PATIENTS AND METHODS

Over a 12-month period, all children with cancer and fever, with or without neutropenia, who were admitted to the NCI for empirical therapy of febrile episodes and who had a microbiologically confirmed bloodstream infection were studied retrospectively.

RESULTS

A total of 328 BSI occurred in 1135 febrile episodes in pediatric cancer patients at the NCI in one year. Gram-positive bacteria were isolated in 168 episodes (51.2%) and 61.9% of the total isolates (either single or mixed), Gram-negative in 97 (29.6%), and mixed infections in 45 (13.7%). The common causative agents of bloodstream infections in this study were coagulase-negative staphylococci (16.2%), Staphylococcus aureus (13.4%), Streptococcus spp. (12.1%) followed by Acinetobacter spp. (6.7%) and Pseudomonas spp. (5.5%). Fungemia was encountered in 18 episodes, being mixed in nine of them. A more serious BSI in terms of a prolonged episode was encountered in 30.2% of the episodes and was significantly associated with patients being hospitalized, having intensified chemotherapy, polymicrobial and fungal infection, lower respiratory tract infections and persistent neutropenia at day seven.

CONCLUSIONS

In a large population of children, common clinical and laboratory risk factors were identified that can help predict more serious BSI. These results encourage the possibility of a more selective management strategy for these children.