Antibiotic resistance in Sudan: assessing the knowledge and practices of healthcare workers in Khartoum.

Background: Antibiotic resistance (ABR) is a major public health issue, associated with increased patient morbidity and mortality globally, with significantly higher rates in low- and middle-income countries (LMICs). Assessment of contextual factors, such as information, education, infrastructure and regulations are important for developing local solutions against ABR. Objectives: To determine the knowledge and practices of healthcare workers (HCWs) towards ABR in hospitals in Sudan. Materials and methods: A survey was conducted in three different hospitals in Khartoum, Sudan from February to December 2020. HCWs of different specialties and expertise were invited to participate. Data were descriptively analysed using Statistical Package for Social Sciences (SPSS). Results: ABR was identified as a big challenge by 89% of 345 HCWs who participated. The results show that 79% of doctors don't rely on the clinical microbiology laboratory (CML) results for antibiotic prescription or clinical decision-making. Sixty percent of HCWs agreed there are infection prevention and control (IPC) guidelines in their hospital, but 74% of them don't have access to them, and infrequently receive relevant IPC training. Furthermore, HCWs obtain ABR information from other colleagues informally, not through local data or reports. Conclusions: Despite adequate knowledge of ABR locally, there are significant contextual technical challenges facing HCWs in Sudan, such as availability of policies and accurate data from CMLs. The results indicate a poor link between HCWs and the CMLs for infection management and it is essential to improve communication between the different hospital departments with regard to ABR transmission, and ensure the effectiveness of local IPC policies based on locally available data.

Klebsiella pneumonia in Sudan: Multidrug Resistance, Polyclonal Dissemination, and Virulence.

The emergence and global expansion of hyper-virulent and multidrug resistant (MDR) Klebsiella pneumoniae is an increasing healthcare threat worldwide. The epidemiology of MDR K. pneumoniae is under-characterized in many parts of the world, particularly Africa. In this study, K. pneumoniae isolates from hospitals in Khartoum, Sudan, have been whole-genome sequenced to investigate their molecular epidemiology, virulence, and resistome profiles. Eighty-six K. pneumoniae were recovered from patients in five hospitals in Khartoum between 2016 and 2020. Antimicrobial susceptibility was performed by disk-diffusion and broth microdilution. All isolates underwent whole genome sequencing using Illumina MiSeq; cgMLST was determined using Ridom SeqSphere+, and 7-loci MLST virulence genes and resistomes were identified. MDR was observed at 80%, with 35 isolates (41%) confirmed carbapenem-resistant. Thirty-seven sequence types were identified, and 14 transmission clusters (TC). Five of these TCs involved more than one hospital. Ybt9 was the most common virulence gene detected, in addition to some isolates harbouring iuc and rmp1. There is a diverse population of K. pneumoniae in Khartoum hospitals, harbouring multiple resistance genes, including genes coding for ESBLs, carbapenemases, and aminoglycoside-modifying enzymes, across multiple ST's. The majority of isolates were singletons and transmissions were rare.

High Levels of Methicillin-Resistant Staphylococcus aureus Carriage Among Healthcare Workers at a Teaching Hospital in Addis Ababa Ethiopia: First Evidence Using mecA Detection.

Background: Staphylococcus aureus is a major human pathogen and causes healthcare and community-acquired infection. Data on the extent of MRSA colonization among health-care workers (HCWs) in sub-Saharan Africa are limited. Hence, we determined the burden of MRSA colonisation among HCWs and administrative staff in Tikur Anbessa Specialised Hospital (TASH), College of Health Sciences (CHS), Addis Ababa University, Ethiopia. Methods: Using a cross-sectional study design, participants were screened for MRSA colonisation between June 2018 and August 2019 using nasal swabs. The swabs were analysed using standard laboratory methods including antibiotic resistance gene, mecA. Anonymised sociodemographic data were collected by pretested questionnaires to evaluate HCWs factors associated with MRSA carriage. Results: A total of 588 HCWs and 468 administrative staff were screened for MRSA. Women were over-represented. Overall, 49.1% (289/588) of HCWs were nurses and 25% (117/468) of the administrative staff were cleaners or laundry workers. Overall, 138 S. aureus isolates were retrieved from the nasal swabs of both groups (16.3%, 96/588 from HCWs). The burden of MRSA colonisation was 4.8% (28/580, 95% CI: 3.1-6.5%) among HCWs compared to 0.2% (1/468, 95% CI: 0.18-0.6%) of administrative staff (p value <0.05). The majority of S. aureus and all MRSA isolates were resistant to penicillin. Isolates from HCWs were more resistant to tested antibiotics than administrative staff (P-value <0.05). Conclusion: This is the first report in Ethiopia on MRSA colonization using mecA and revealed that; (i) overall carriage rates of MRSA in HCWs are comparable with observations reported in some other countries and (ii) HCWs exhibit a higher burden of MRSA carriage than administrative staff. Our data support strategic screening of MRSA and antimicrobial stewardship for better intervention measures.

Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii From Khartoum State, Sudan.

Carbapenem resistant Acinetobacter baumannii (CRAb) is an important global pathogen contributing to increased morbidity and mortality in hospitalized patients, due to limited alternative treatment options. Nine international clonal (IC) lineages have been identified in many countries worldwide, however, data still lacks from some parts of the world, particularly in Africa. We hereby present the molecular epidemiology of MDR A. baumannii from four hospitals in Khartoum, Sudan, collected from 2017 to 2018. Forty-two isolates were whole-genome sequenced, and subsequent molecular epidemiology was determined by core genome MLST (cgMLST), and their resistomes identified. All isolates had an array of diverse antibiotic resistance mechanisms conferring resistance to multiple classes of antibiotics. We found a predominance (88%) of IC2 (with the intrinsic OXA-66 and acquired OXA-23), and some with NDM-1. IC2 isolates were sub-divided into 4 STs separated by 5 to 431 allelic differences, and with evidence of seven transmission clusters. Isolates belonging to IC1, IC5, and IC9 were also identified. These data illustrate that MDR IC2 A. baumannii are widely distributed in Khartoum hospitals and are in possession of multiple antibiotic resistance determinants.

Multiclonal spread of Klebsiella pneumoniae across hospitals in Khartoum, Sudan.

OBJECTIVES: Multidrug-resistant (MDR) Klebsiella pneumoniae is increasing worldwide with poorly characterised epidemiology in many parts of the world, particularly in Africa. This study aimed to investigate the molecular epidemiology of K. pneumoniae, to identify the diversity of sequence types (ST), and to detect carbapenem resistance genes in major regional hospitals in Khartoum, Sudan. METHODS: Klebsiella pneumoniae isolates (n = 117) were cultured from four hospitals in Khartoum, from April 2015 to October 2016. The isolates were characterised by sequencing of 16S-23S rDNA internal transcribed spacer (ITS) region. Molecular epidemiology was determined by multilocus sequence typing (MLST), and analysed by maximum likelihood phylogeny (PhyML). Antimicrobial susceptibility was determined by disk diffusion. Isolates phenotypically resistant to carbapenem were screened for carbapenemase genes: blaNDM, blaOXA48, blaIMP, blaVIM and blaGES by PCR. RESULTS: ITS sequencing confirmed the 117 isolates as K. pneumoniae. MLST revealed 52 different STs grouped in four distinct clusters by PhyML. All isolates were MDR, and carbapenemase-producing K. pneumoniae (CP-KP) isolates accounted for 44/117 (37.6%) mostly harbouring blaNDM (28/44) and blaOXA-48 (7/44), with several isolates harbouring multiple genes. CONCLUSION: MDR and CP-KP K. pneumoniae is widespread in Khartoum hospitals, with a diverse population of 52 STs clustering in four major lineages. There is an urgent need for systematic epidemiological studies of drug-resistant infections across all healthcare institutions in Sudan to inform local infection prevention and control strategies.

Comparing conventional, biochemical and genotypic methods for accurate identification of Klebsiella pneumoniae in Sudan.

Klebsiella pneumoniae is recognized as one of the most important healthcare-associated pathogens worldwide due to its tendency to develop antibiotic resistance and cause fatal outcomes. Bacterial identification methods such as culture and biochemical tests are routinely used with limited accuracy in many low- and middle-income countries, including Sudan. The aim of this study was to test the accuracy of identification of K. pneumoniae in Khartoum, Sudan. Two hundred and fifty K. pneumoniae isolates were collected and identified using conventional phenotypic methods, biochemically using API 20E and genotypically by amplification of 16S-23S rDNA and sequencing of rpoB, gapA and pgi. Only 139 (55.6 %) of the isolates were confirmed as K. pneumoniae genotypically by PCR and 44.4 % were identified as non- K. pneumoniae . The results demonstrate that the identification panels used by the hospitals were inaccurately identifying K. pneumonia and led to overestimation of the prevalence of this organism. The current identification methods used in Khartoum hospitals are highly inaccurate, and therefore we recommend the use of a comprehensive biochemical panel or molecular methods, when possible, for accurate identification of K. pneumoniae .

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.

Detection of several carbapenems resistant and virulence genes in classical and hyper-virulent strains of Klebsiella pneumoniae isolated from hospitalized neonates and adults in Khartoum.

OBJECTIVE: Klebsiella pneumoniae (K. pneumoniae) involves both community-acquired and nosocomial infections. It is responsible for a wide variety of infections, including infections of the urinary tract, pneumonia, bacteremia, meningitis, wound infection and purulent abscesses. We constructed this study to detect several carbapenems resistant and virulence genes in classical and hyper-virulent strains of K. pneumoniae isolated from hospitalized neonates and adults in Khartoum state. RESULTS: Seventy percent of the isolates were resistant to ceftazidime, 18(30%) to ciprofloxacin, 23(38.3%) to chloramphenicol, 24(40%) to gentamicin and 8% to imipenem, 35% were multidrug-resistant, and 7% extensively drug-resistant, all blood isolates (n = 14) were resistant to ceftazidime. entB was the most predominant virulence gene (93.3%), followed by mrkD (78.3%), kfu (60%), K2 (51.7%), magA (18.3%) and rmpA (5%). blaOXA-48 was the most predominant carbapenem-resistant gene (68.3%), followed by blaNDM (10%), blaKPC (8.3%), and blaIMP (3.3%). Eight hyper-virulent strains were positive for blaOXA-48 and two for blaNDM genes.

Molecular characterisation of an Acinetobacter baumannii outbreak.

BACKGROUND: Acinetobacter baumannii are problematic hospital pathogens, and the increased incidence of multi drug resistance has significantly limited treatment options. The global epidemiology is not fully characterised due to large data gaps from low- and middle-income countries. This study characterised the molecular epidemiology of an A. baumanniii outbreak in Egypt. METHODS: Fifty-four A. baumannii isolates were recovered from a 4-month-outbreak at Tanta University Hospitals (TUH). Associated clinical and demographic data, and the antibiograms were analysed, and Carbapenem resistant isolates were screened for acquired carbapenemase genes by PCR and sequencing. Epidemiological typing was performed by single-locus sequencing of bla OXA-51-like and Multi Locus Sequence Typing (MLST), and sequence types (STs) were analysed based on maximum-likelihood phylogeny (PhyML) to identify relatedness. FINDINGS: Immune suppression and ICU admission were the most common co-morbidity and risk factor. Carbapenem resistance accounted for 81%, and correlated with the presence of OXA-23, NDM-1 and -2, and VIM-1 and -2 carbapenemases. Nine different bla OXA-51-like genes were identified which corresponded to 22 different Sequence Types (STs), including 10 novel. International clone (IC2) was the predominant clone. PhyML analysis revealed the presence of 2 distinct clones with multiple sub-lineages. CONCLUSION: Given the short duration of the study, there was a rare heterogeneous population in the hospital. Carbapenem resistance is mediated by acquired carbapenemases in diverse lineages indicating the possibility of horizontal gene transfer. The diversity indicates the influx of multiple lineages of IC2 into TUH from unknown sources. Molecular epidemiological studies are essential for infection prevention and control measures.

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 blaOXA-23, blaOXA-58, blaNDM-1 and blaVIM-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.

Variations in IS6 promoters alter the expression of carbapenem resistance in related strains of Acinetobacter baumannii.

The aim of this work was to investigate the role of the IS6 family of insertion sequences present upstream of blaOXA-58 in two clonally related carbapenem-resistant Acinetobacter baumannii isolates obtained from paediatric cancer patients in Egypt. To determine their relatedness, the isolates were typed by pulsed-field gel electrophoresis (PFGE), and the intrinsic blaOXA-51-like gene was amplified and sequenced. Minimum inhibitory concentrations (MICs) to imipenem and meropenem was determined according to British Society of Antimicrobial Chemotherapy (BSAC) guidelines. PCR and sequencing of blaOXA-58 and the upstream and downstream regions was performed to determine the genetic environment. The two isolates were positive for the intrinsic blaOXA-64 gene, and the MICs for isolates AB-14298 and AB-P67 were 8mg/L and 64mg/L for imipenem and 2mg/L and 16mg/L for meropenem, respectively. The blaOXA-58 gene in AB-14298 was flanked by ISAba3 interrupted with IS1006, whereas AB-P67 had ISAba3 interrupted by IS1008, both belonging to the IS6 family of insertion sequences. In conclusion, both IS1006 and IS1008 provided suitable promoter sequences for expression of the downstream blaOXA-58 gene.

Epidemiology of Acinetobacter baumannii of animal origin.

Acinetobacter baumannii is an opportunistic pathogen responsible for nosocomial infections, however the origins of these bacteria remain unclear. Sixteen A. baumannii strains collected from animals slaughtered for human consumption were investigated for their susceptibility profiles, resistance islands (RIs), class 1 integrons, insertion sequence ISAba1, and bla(OXA-51)-like and bla(AmpC) genes. Polymerase chain reaction (PCR) and sequencing approaches were used to identify and type the isolates using the intrinsic gene bla(OXA-51)-like genes. Genotyping was also performed by pulsed-field gel electrophoresis (PFGE) to establish whether there was a genetic relationship between animal isolates and the main human isolates of European clones I, II and III (ECI, ECII and ECIII) known to cause major hospital outbreaks. All 16 isolates (100%) were sensitive to carbapenems, gentamicin, ciprofloxacin and piperacillin/tazobactam but were resistant to amoxicillin, cefradine, trimethoprim and chloramphenicol. Moreover, all isolates had a baseline resistance to ceftazidime, with a minimum inhibitory concentration of 4 mg/L. All isolates lacked RIs, ISAba1 and class 1 integrons but harboured bla(OXA-51)-like and bla(AmpC) genes. In addition, this study reports for the first time three new bla(OXA-51)-like genes (bla(OXA-148), bla(OXA-149) and bla(OXA-150)) isolated from bacteria in cattle, which have not been found previously in human isolates. However, all isolates recovered from pig faecal samples harboured one type of bla(OXA-51)-like (bla(OXA-51) itself), which has already been reported in human clinical isolates. From sequencing of the bla(OXA-51)-like genes from animal isolates, it was possible to identify four different clusters similar to those identified by PFGE, which in turn also distinguished these four groups from the human ECI, ECII and ECIII strains.