Genomic Characterization of Uropathogenic Escherichia coli Isolates from Tertiary Hospitals in Riyadh, Saudi Arabia.

Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infections (UTIs) in hospitalised and non-hospitalised patients. Genomic analysis was used to gain further insight into the molecular characteristics of UPEC isolates from Saudi Arabia. A total of 165 isolates were collected from patients with UTIs between May 2019 and September 2020 from two tertiary hospitals in Riyadh, Saudi Arabia. Identification and antimicrobial susceptibility testing (AST) were performed using the VITEK system. Extended-spectrum ß-lactamase (ESBL)-producing isolates (n = 48) were selected for whole genome sequencing (WGS) analysis. In silico analysis revealed that the most common sequence types detected were ST131 (39.6%), ST1193 (12.5%), ST73 (10.4%), and ST10 (8.3%). Our finding showed that blaCTX-M-15 gene was detected in the majority of ESBL isolates (79.2%), followed by blaCTX-M-27 (12.5%) and blaCTX-M-8 (2.1%). ST131 carried blaCTX-M-15 or blaCTX-M-27, and all ST73 and ST1193 carried blaCTX-M-15. The relatively high proportion of ST1193 in this study was notable as a newly emerged lineage in the region, which warrants further monitoring.

Antibiotic-resistant ST38, ST131 and ST405 strains are the leading uropathogenic Escherichia coli clones in Riyadh, Saudi Arabia.

OBJECTIVES: We investigated the molecular epidemiology of uropathogenic Escherichia coli (UPEC) from a tertiary care hospital in Riyadh, Saudi Arabia, revealing, for the first time, the population structure of UPEC in the region. METHODS: A total of 202 UPEC isolates were recovered from hospital and community patients with urinary tract infection in December 2012 and January 2013. Strains were characterized by MLST, antibiotic susceptibility determination and virulence gene detection. RESULTS: The most common lineages were ST131 (17.3%), ST73 (11.4%), ST38 (7.4%), ST69 (7.4%), ST10 (6.4%), ST127 (5.9%), ST95 (5.4%), ST12 (3.5%), ST998 (3.5%) and ST405 (3%). ST131 and ST405 isolates were significantly associated with high levels of antibiotic resistance (60% of ST131 carried CTX-M-14 or CTX-M-15 and 66.7% of ST405 isolates carried CTX-M-15). ST131, CTX-M-15-positive isolates were predominantly of the fimH30/clade C group, resistant to fluoroquinolones; members of this sub-group were more likely to carry a high number of genes encoding selected virulence determinants. The relatively high proportion of ST38 was notable and four of these isolates harboured aggR. CONCLUSIONS: Our findings highlight the presence of MDR, CTX-M-positive ST38, ST131 and ST405 UPEC in Saudi Arabia. The high proportion of isolates with CTX-M is a particular concern. We suggest that ST38 UPEC warrant further study.

Antivirulence Effects of Trans-Resveratrol and Curcumin on Methicillin-Resistant Staphylococcus aureus (MRSA) from Saudi Arabia.

Methicillin-resistant Staphylococcus aureus (MRSA) is a common resistant bacterium, whose resistance has expanded to commonly used antibiotics. It is crucial to create novel treatments to tackle bacterial resistance. Trans-resveratrol and curcumin are naturally occurring phenolic compounds, whose effects on MRSA virulence are the subject of this investigation. Sub-MICs of trans-resveratrol and curcumin were tested on the virulence factors of 50 MRSA clinical isolates (CIs), including biofilm, hemolysin, hemagglutination, protease, and lecithinase. The distribution of the virulence factors of the CIs was as follows: hemolysin: 98%, hemagglutination: 70%, protease: 62%, biofilm: 56%, and lecithinase: 52%. The sub-MIC that could reduce the effect of the tested virulence factors by 50% or more (IC50) was observed in the strains that showed susceptibility to the individual administration of trans-resveratrol at 50 µg/mL and curcumin at 20 µg/mL. Hemagglutination and hemolysin activity were inhibited by at least 50% in the majority of CIs (57-94%). Meanwhile, the IC50 for protease and biofilm was observed in 6.5-17.8% of the CIs. A few of the CIs were susceptible to lecithinase inhibition, but all showed a full inhibition. This research supports the possibility of the use of these compounds to reduce the bacterial virulence that can reduce antibiotic utilization, and eventually, they can become a potential alternative treatment in combating bacterial resistance.

Effect of Resveratrol and Curcumin on Gene Expression of Methicillin-Resistant Staphylococcus aureus (MRSA) Toxins.

Staphylococcus aureus is an opportunistic pathogen that can lead to a number of potentially terrible community- and hospital-acquired illnesses. Among the diverse set of virulence factors that S. aureus possesses, secreted toxins play a particularly preeminent role in defining its virulence. In this work, we aimed to facilitate the development of novel strategies utilizing natural compounds to lower S. aureus's toxin production and consequently enhance therapeutic approaches. Two natural polyphenols, resveratrol (RSV) and curcumin (CUR), were tested for their effect on reducing toxin gene production of MRSA isolates. Fifty clinical MRSA isolates were gathered from Riyadh and Jeddah. Molecular screening of toxin genes (sea, seb, sec, sed, seh, lukF, and lukS) harbored by MRSA was performed. Sub-inhibitory concentrations of RSV (50 µg/ml) and CUR (20 µg/ml) were determined to study their effect on the gene expression MRSA's toxin genes. Our findings revealed the presence of the tested genes in MRSA isolates, with lukF being the most prevalent gene and seh the least detected gene. We found that RSV reduced the relative expression of toxin genes, sea, seb, lukF, and lukS, respectively, while CUR decreased the relative expression of sea and seb genes in the examined isolates. Regarding lukF and lukS, CUR downregulated the expression of both genes in some isolates and upregulated the expression in other isolates. From these results, we concluded that RSV and CUR could be used as alternative therapeutic approaches to treat MRSA infections through reducing toxin production.

The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years.

BACKGROUND: Klebsiella pneumoniae is a major bacterial and opportunistic human pathogen, increasingly recognized as a healthcare burden globally. The convergence of resistance and virulence in K. pneumoniae strains has led to the formation of hypervirulent and multidrug-resistant strains with dual risk, limiting treatment options. K. pneumoniae clones are known to emerge locally and spread globally. Therefore, an understanding of the dynamics and evolution of the emerging strains in hospitals is warranted to prevent future outbreaks. METHODS: In this study, we conducted an in-depth genomic analysis on a large-scale collection of 328 multidrug-resistant (MDR) K. pneumoniae strains recovered from 239 patients from a single major hospital in the western coastal city of Jeddah in Saudi Arabia from 2014 through 2022. We employed a broad range of phylogenetic and phylodynamic methods to understand the evolution of the predominant clones on epidemiological time scales, virulence and resistance determinants, and their dynamics. We also integrated the genomic data with detailed electronic health record (EHR) data for the patients to understand the clinical implications of the resistance and virulence of different strains. RESULTS: We discovered a diverse population underlying the infections, with most strains belonging to Clonal Complex 14 (CC14) exhibiting dominance. Specifically, we observed the emergence and continuous expansion of strains belonging to the dominant ST2096 in the CC14 clade across hospital wards in recent years. These strains acquired resistance mutations against colistin and extended spectrum ß-lactamase (ESBL) and carbapenemase genes, namely blaOXA-48 and blaOXA-232, located on three distinct plasmids, on epidemiological time scales. Strains of ST2096 exhibited a high virulence level with the presence of the siderophore aerobactin (iuc) locus situated on the same mosaic plasmid as the ESBL gene. Integration of ST2096 with EHR data confirmed the significant link between colonization by ST2096 and the diagnosis of sepsis and elevated in-hospital mortality (p-value < 0.05). CONCLUSIONS: Overall, these results demonstrate the clinical significance of ST2096 clones and illustrate the rapid evolution of an emerging hypervirulent and MDR K. pneumoniae in a clinical setting.

In vitro activity of cefiderocol against clinically important carbapenem non-susceptible Gram-negative bacteria from Saudi Arabia.

OBJECTIVES: Cefiderocol is a novel catechol-substituted siderophore cephalosporin with broad-spectrum activity against Gram-negative pathogens. However, variation of its activity among carbapenemase producers from various regions and countries has been reported. Here, we checked the in vitro activity against Gram-negative carbapenem non-susceptible bacteria collected in Saudi Arabia. METHODS: Cefiderocol MICs were determined using the iron-depleted cation-adjusted Mueller-Hinton broth and interpreted according to the Clinical and Laboratory Standards Institute guidelines. Isolates (n = 288) included carbapenemase-producing Escherichia coli (n = 46), Klebsiella pneumoniae (n = 98), Acinetobacter baumannii (n = 65), and Pseudomonas aeruginosa (n = 79) clinical isolates. RESULTS: Cefiderocol inhibited 73.26% (211/288) of the isolates studied at concentrations of ≤ 4 mg/L. Cefiderocol inhibited all carbapenem-resistant A. baumannii isolates (65/65, 100%) producing OXA-23-like, OXA-24-like, and NDM, and nearly all P. aeruginosa isolates (75/79, 94.94%), including those producing VIM and NDM. In contrast, the carbapenemase-producing isolates from the Enterobacterales group demonstrated significantly higher MICs with only 53.06% (52/98) of K. pneumoniae and 41.3% (19/46) of E. coli isolates exhibiting MICs of ≤4 mg/L. Isolates showing elevated MICs (73/144, 50.69%) included NDM (20/29, 68.97%), NDM/OXA-48-like (34/59, 57.63%), OXA-48-like (18/52, 34.62%), and KPC (1/4, 25%) producers, thus showing no clear association with the production of serine-type or metallo-type carbapenemases. However, high cefiderocol MICs (≥ 32mg/L) were associated with isolates producing NDM, and in particular, among those coproducing the OXA-232-type enzyme. CONCLUSIONS: Cefiderocol had excellent activity against multi-drug resistant non-fermenting Gram-negative pathogens. Reasons behind the high cefiderocol MICs in certain Enterobacterales isolates need further investigation.

Prevalence of Carbapenem Non-susceptible Gram-Negative Bacteria at Tertiary Care Hospitals in Saudi Arabia.

Background Antibiotics significantly increased life expectancy and decreased mortality rates due to infections. However, this trend is starting to fade with the rise of multidrug-resistant organisms (MDR); these strains are becoming a global burden on healthcare and the economy. The dramatic increase and spread of carbapenem-resistant gram-negative bacteria (CRGNB) has become a serious global public health concern. In this retrospective cross-sectional study, we aimed to estimate the rates of gram-negative bacteremia in five tertiary care hospitals in different geographical locations in Saudi Arabia for five years. Methods A retrospective cross-sectional study was conducted in five tertiary care hospitals in Saudi Arabia among patients with bacteremia due to CRGNB. Electronic medical records were used to retrieve data regarding patient demographics and antimicrobial susceptibility testing (AST) over five years between January 2016 and December 2020. Patients with positive blood cultures for carbapenem-resistant Escherichia (E.) coli, Klebsiella (K.) pneumonia, Pseudomonas (P.) aeruginosa, and Acinetobacter (A.) baumannii comprise the final study population. Results This retrospective multicentric study was conducted between 2016 and 2020 in five tertiary care hospitals across five cities in Saudi Arabia. E. coli (n=2190, 38.03%), K. pneumoniae (n=2154, 37.41%), P. aeruginosa (n = 918, 15.94%), and A. baumannii (n=496, 8.61%) constitute the 5758 gram-negative bacteria isolates. E. coli was the most frequently identified species in Riyadh, AlAhsa, Dammam, and Madinah (40%, 46.50%, 61.67%, and 43.66%, respectively), with a p-value of (p<0.001), except in Jeddah, where K. pneumoniae was the most prevalent (42%). The mean age of patients across Riyadh, AlAhsa, Dammam, and Madinah was 62.2 years (± 4.24). In contrast to Jeddah, where the majority of isolates (702; 41.8%) belonged to the adult age group. Most isolates were from male patients (3045; 52.9%), compared to 2713 (47.1%) from female patients. K. pneumoniae 1226 (40.3%) was the most prevalent isolate among male patients while E. coli (1135; 41.8%) was the most prevalent isolate among female patients. Conclusion Our study showed that the prevalence of carbapenem non-susceptible Gram-negative bacteria is relatively high, which therefore makes them very challenging to treat. The results show an urgent need for improved antibiotic stewardship strategies, including better surveillance and more effective infection control measures to reduce this issue. Further research into the molecular epidemiology and risk factors associated with these infections is necessary to guide public health policymakers in developing interventions to help control the spread of carbapenem-resistant Gram-negative bacteria.

Molecular characterization and differential effects of levofloxacin and ciprofloxacin on the potential for developing quinolone resistance among clinical Pseudomonas aeruginosa isolates.

Background: Fluoroquinolones are some of the most used antimicrobial agents for the treatment of Pseudomonas aeruginosa. This study aimed at exploring the differential activity of ciprofloxacin and levofloxacin on the selection of resistance among P. aeruginosa isolates at our medical center. Methods: 233 P. aeruginosa clinical isolates were included in this study. Antimicrobial susceptibility testing (AST) was done using disk diffusion and broth microdilution assays. Random Amplification of Polymorphic DNA (RAPD) was done to determine the genetic relatedness between the isolates. Induction of resistance against ciprofloxacin and levofloxacin was done on 19 isolates. Fitness cost assay was done on the 38 induced mutants and their parental isolates. Finally, whole genome sequencing was done on 16 induced mutants and their 8 parental isolates. Results: AST results showed that aztreonam had the highest non-susceptibility. RAPD results identified 18 clusters. The 19 P. aeruginosa isolates that were induced against ciprofloxacin and levofloxacin yielded MICs ranging between 16 and 256 µg/mL. Levofloxacin required fewer passages in 10 isolates and the same number of passages in 9 isolates as compared to ciprofloxacin to reach their breakpoints. Fitness cost results showed that 12 and 10 induced mutants against ciprofloxacin and levofloxacin, respectively, had higher fitness cost when compared to their parental isolates. Whole genome sequencing results showed that resistance to ciprofloxacin and levofloxacin in sequenced mutants were mainly associated with alterations in gyrA, gyrB and parC genes. Conclusion: Understanding resistance patterns and risk factors associated with infections is crucial to decrease the emerging threat of antimicrobial resistance.

Antimicrobial resistance and genomic characterization of Salmonella enterica isolates from chicken meat.

This study investigated genotypic and phenotypic antimicrobial resistance profiles, phylogenic relatedness, plasmid and virulence composition of 39 Salmonella enterica strains isolated from chicken meat samples using whole genome sequencing (WGS) technology. Four distinct serotypes were identified; Salmonella Minnesota (16/39, 41%), Salmonella Infantis (13/39, 33.3%), Salmonella Enteritidis (9/39, 23.1%), and one isolate was detected for Salmonella Kentucky (1/39, 2.6%), with sequence types (STs) as followed: ST548, ST32, ST11, and ST198, respectively. Phenotypic resistance to tetracycline (91.2%), ampicillin (82.4%), sulfisoxazole (64.7%), and nalidixic acid (61.6%) was the most observed. Resistome analysis revealed the presence of resistance genes to aminoglycosides, ß-lactamase, sulfonamides, trimethoprim, phenicol, lincosamide, macrolides, and tetracyclines. Plasmidome showed the presence of eight incompatibility groups, including IncA/C2, IncFIB(K)_1_Kpn3, Col440I_1, IncR, IncX1, IncI1_1_Alpha, IncFIB(S)/IncFII(S), IncHI2/IncHI2A, IncX2 and ColpVC plasmids across the 39 genomes. Three resistance genes, sul2, tetA and blaCMY-2, were predicted to be located on IncA/C2 plasmid in S. Minnesota isolates, whereas all S. Infantis isolates were positive to IncFIB(K)_1_Kpn3 plasmid that carries bla CTX-M-65 gene. Eleven Salmonella pathogenicity islands and up to 131 stress and/or virulence genes were identified in the evaluated genomes. Phylogenetic analysis showed four phylogroups that were consistent with the identified ST profiles with a high level of inter-diversity between isolates. This is the first genomic characterization of Salmonella isolates from retail chicken meat in Saudi Arabia using WGS technology. The availability of Salmonella genomes from multiple geographic locations, including Saudi Arabia, would be highly beneficial in future source-tracking, especially during epidemiological surveillance and outbreak investigations.

Towards promising antimicrobial alternatives: The future of bacteriophage research and development in Saudi Arabia.

The escalating threat of antibiotic-resistant pathogens resulting from the rapid emergence of antimicrobial resistance (AMR) is a significant health and economic concern worldwide, exacerbated by the misuse of antibiotics in both humans and livestock. This has led to critical challenges when treating infections by multi-drug resistant (MDR) pathogens, which often display high mortality and morbidity rates. An international action plan and multisectoral cooperative approach are therefore needed to combat and halt AMR dissemination. Critical to these efforts are enhanced research programs aimed at identifying new antimicrobial agents, as well as the use of advanced biotechnology tools to develop alternative antimicrobial approaches. Bacteriophages (phages)-viruses that infect and kill bacteria-represent a promising tool for combatting the global threat of antibiotic-resistant pathogens. Phages and their potential applications have been extensively studied in Europe and the United States (US) for decades. However, although health authorities in the Gulf Health Council (GHC), including Saudi Arabia, have developed an action plan to combat AMR, phage research in the Middle East has lagged behind global scientific efforts. Thus, there is still a paucity of phage-related studies in this region, including those focused on therapeutic applications, clinical trials, biotechnology, and biocontrol. This article highlights the importance of bacteriophage research and development and discusses the potential implementation of phage-based therapies in Saudi Arabia.

Development and Evaluation of Enzyme-Linked Viral Immune Capture Assay for Detection of SARS-CoV-2.

The pandemic of COVID-19 was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 and it has prompted unprecedented research activities for vaccines, therapeutics, and diagnostics. The real-time reverse transcriptase-polymerase chain reaction (RT-PCR) is the gold standard method of diagnosis; however, immune-based assays offer cost-effective, deployable, easy-to-read solutions for diagnosis and surveillance. Here, we present the development, optimization, and testing of an enzyme-linked viral immune capture assay (ELVICA). It utilizes the spike antigen as the detected target of the virus and antibody-coated beads to capture the virus and enrich the detection. This method can be readout by luminescent and colorimetric equipment. It can also be visualized by the imaging system, offering a variety of detection approaches. ELVICA showed specificity to SARS-CoV-2-pseudotyped viruses as compared to MERS-CoV-pseudotyped viruses. As compared to RT-PCR, ELVICA showed high compatibility in detecting the virus in patient respiratory samples, especially for samples that are below a Ct value of 32 in RT-PCR. This assay is readily adaptable for detecting other pathogens and serves as a quick and affordable diagnostic tool.

Antibacterial Efficacy of Liposomal Formulations Containing Tobramycin and N-Acetylcysteine against Tobramycin-Resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii.

The antibacterial activity and biofilm reduction capability of liposome formulations encapsulating tobramycin (TL), and Tobramycin-N-acetylcysteine (TNL) were tested against tobramycin-resistant strains of E. coli, K. pneumoniae and A. baumannii in the presence of several resistant genes. All antibacterial activity were assessed against tobramycin-resistant bacterial clinical isolate strains, which were fully characterized by whole-genome sequencing (WGS). All isolates acquired one or more of AMEs genes, efflux pump genes, OMP genes, and biofilm formation genes. TL formulation inhibited the growth of EC_089 and KP_002 isolates from 64 mg/L and 1024 mg/L to 8 mg/L. TNL formulation reduced the MIC of the same isolates to 16 mg/L. TNL formulation was the only effective formulation against all A. baumannii strains compared with TL and conventional tobramycin (in the plektonic environment). Biofilm reduction was significantly observed when TL and TNL formulations were used against E. coli and K. pneumoniae strains. TNL formulation reduced biofilm formation at a low concentration of 16 mg/L compared with TL and conventional tobramycin. In conclusion, TL and TNL formulations particularly need to be tested on animal models, where they may pave the way to considering drug delivery for the treatment of serious infectious diseases.

Acquired resistome and plasmid sequencing of mcr-1 carrying MDR Enterobacteriaceae from poultry and their relationship to STs associated with humans.

OBJECTIVES: To investigate the acquired resistome in 18 colistin-resistant Escherichia coli isolated from different poultry farms in Lebanon, analyse Inc plasmids associated with mcr and assess potential transmission to humans. METHODS: A total of 18 E. coli were recovered from poultry faeces collected from different poultry farms in Lebanon. Broth microdilution (BMD) assay was performed to determine the antimicrobial resistance profiles. WGS was used to identify the genetic determinants behind the resistance in these isolates. RESULTS: BMD results showed that all of the 18 isolates were colistin resistant. Furthermore, resistance to trimethoprim/sulfamethoxazole was the most recorded among the isolates and only one isolate was resistant to cefepime. Sequencing results showed that the isolates were distributed into seven different STs and that the most abundant was ST1140. The number of antimicrobial resistant determinants ranged from 4 to 21 among the 18 isolates, with tet(A) and floR being the most frequent. Moreover, a total of 15 different plasmid replicon types were identified. The mcr-1 gene was shown to be predominantly located on IncX4 plasmids. Additionally, two isolates harboured the IncI2-type self-conjugative plasmid. CONCLUSIONS: The findings show that mcr and other important resistance determinants occur in MDR E. coli isolated poultry farms in Lebanon. The occurrence of mcr on mobile plasmids and the zoonotic potential and clinical relevance of some strains highlight a risk of transmission to humans.

Epidemiological and molecular description of nosocomial outbreak of COVID-19 Alpha (B.1.1.7) variant in Saudi Arabia.

BACKGROUND: Nosocomial outbreaks frequently occurred during the Coronavirus disease 2019 (COVID-19) pandemic; however, sharing experiences on outbreak containment is vital to reduce the related burden in different locations. OBJECTIVES: This article aims at sharing a practical experience on COVID-19 outbreak containment, including contact tracing, screening of target population, testing including molecular analysis, and preventive modalities. It also provides an epidemiological and molecular analysis of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS­CoV­2) infection outbreak in a tertiary care hospital in Saudi Arabia. METHODS: The outbreak occurred in a non-COVID medical ward at a tertiary care hospital in Jeddah, Saudi Arabia, from 22nd March and 15th April 2021. The multidisciplinary outbreak response team performed clinical and epidemiological investigations. Whole-Genome Sequencing (WGS) was implemented on selected isolates for further molecular characterization. RESULTS: A total of eight nurses (20 % of the assigned ward nurses) and six patients (16.2 % of the ward admitted patients at the time of the outbreak) tested positive for the SARS-CoV-2 virus based on PCR testing. The outbreak investigation identified strong evidence of an epidemiologic link between the affected cases. WGS revealed a set of spike mutations and deletions specific to the Alpha variant (B.1.1.7 lineage). All the nurses had mild symptoms, and the fatality among the patients was 50 % (three out of the six patients). CONCLUSIONS: The current nosocomial COVID-19 outbreak, caused by the Alpha variant, revealed multiple breaches in the adherence to the hospital infection control recommended measures. Containment strategies were successful in controlling the outbreak and limiting infection spread. Molecular analysis and genome sequencing are essential tools besides epidemiological investigation to inform appropriate actions, especially with emerging pathogens.

Establishing a marine monitoring programme to assess antibiotic resistance: A case study from the Gulf Cooperation Council (GCC) region.

The World Health Organization considers antimicrobial resistance as one of the most pressing global issues which poses a fundamental threat to human health, development, and security. Due to demographic and environmental factors, the marine environment of the Gulf Cooperation Council (GCC) region may be particularly susceptible to the threat of antimicrobial resistance. However, there is currently little information on the presence of AMR in the GCC marine environment to inform the design of appropriate targeted surveillance activities. The objective of this study was to develop, implement and conduct a rapid regional baseline monitoring survey of the presence of AMR in the GCC marine environment, through the analysis of seawater collected from high-risk areas across four GCC states: (Bahrain, Oman, Kuwait, and the United Arab Emirates). 560 Escherichia coli strains were analysed as part of this monitoring programme between December 2018 and May 2019. Multi-drug resistance (resistance to three or more structural classes of antimicrobials) was observed in 32.5% of tested isolates. High levels of reduced susceptibility to ampicillin (29.6%), nalidixic acid (27.9%), tetracycline (27.5%), sulfamethoxazole (22.5%) and trimethoprim (22.5%) were observed. Reduced susceptibility to the high priority critically important antimicrobials: azithromycin (9.3%), ceftazidime (12.7%), cefotaxime (12.7%), ciprofloxacin (44.6%), gentamicin (2.7%) and tigecycline (0.5%), was also noted. A subset of 173 isolates was whole genome sequenced, and high carriage rates of qnrS1 (60/173) and bla CTX-M-15 (45/173) were observed, correlating with reduced susceptibility to the fluoroquinolones and third generation cephalosporins, respectively. This study is important because of the resistance patterns observed, the demonstrated utility in applying genomic-based approaches to routine microbiological monitoring, and the overall establishment of a transnational AMR surveillance framework focussed on coastal and marine environments.

Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients.

In December 2019, the emergence of SARS-CoV-2 virus in China led to a pandemic. Since both Influenza Like Illness (ILI) and COVID-19 case definitions overlap, we re-investigated the ILI cases using PCR for the presence of SARS-CoV-2 in 739 nasopharyngeal swabs collected from November 2019 to March 2020. SARS-CoV-2 RNA was found in 37 samples (5%) collected mostly during February 2020. It was followed by confirmation of evolutionary and spatial relationships using next generation sequencing (NGS). We observed that the overall incidence of ILI cases during 2019-2020 influenza season was considerably higher than previous years and was gradually replaced with SARS-CoV-2, which indicated a silent transmission among ambulatory patients. Sequencing of representative isolates confirmed independent introductions and silent transmission earlier than previously thought. Evolutionary and spatial analyses revealed clustering in the GH clade, characterized by three amino acid substitutions in spike gene (D614G), RdRp (P323L) and NS3 (Q57H). P323L causes conformational change near nsp8 binding site that might affect virus replication and transcription. In conclusion, assessment of the community transmission among patients with mild COVID-19 illness, particularly those without epidemiological link for acquiring the virus, is of utmost importance to guide policy makers to optimize public health interventions. The detection of SARS-CoV-2 in ILI cases shows the importance of ILI surveillance systems and warrants its further strengthening to mitigate the ongoing transmission of SARS-CoV-2. The effect of NS3 substitutions on oligomerization or membrane channel function (intra- and extracellular) needs functional validation.

Learning From Mistakes: The Role of Phages in Pandemics.

The misuse of antibiotics is leading to the emergence of multidrug-resistant (MDR) bacteria, and in the absence of available treatments, this has become a major global threat. In the middle of the recent severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic, which has challenged the whole world, the emergence of MDR bacteria is increasing due to prophylactic administration of antibiotics to intensive care unit patients to prevent secondary bacterial infections. This is just an example underscoring the need to seek alternative treatments against MDR bacteria. To this end, phage therapy has been proposed as a promising tool. However, further research in the field is mandatory to assure safety protocols and to develop appropriate regulations for its use in clinics. This requires investing more in such non-conventional or alternative therapeutic approaches, to develop new treatment regimens capable of reducing the emergence of MDR and preventing future global public health concerns that could lead to incalculable human and economic losses.

Management of Candida auris outbreak in a tertiary-care setting in Saudi Arabia.

OBJECTIVE: To describe local experience in managing an outbreak of Candida auris in a tertiary-care setting. METHODS: In response to emerging Candida auris, an outbreak investigation was conducted at our hospital between March 2018 and June 2019. Once a patient was confirmed to have Candida auris, screening of exposed patients and healthcare workers (HCWs) was conducted. Postexposure screening included those who had had direct contact with or shared the same unit or ward with a laboratory-confirmed case. In response to the increasing number of cases, new infection control measures were implemented. RESULTS: In total, 23 primary patients were detected over 15 months. Postexposure screening identified 11 more cases, and all were patients. Furthermore, ~28.6% of patients probably caught infection in another hospital or in the community. Infection control measures were strictly implemented including hand hygiene, personal protective equipment, patient hygiene, environmental cleaning, cohorting of patients and HCWs, and avoiding the sharing of equipment. The wave reached a peak in April 2019, followed by a sharp decrease in May 2019 and complete clearance in June 2019. The case patients were equally distributed between intensive care units (51.4%) and wards (48.6%). More infections (62.9%) occurred than colonizations (37.1%). Urinary tract infection (42.9%) and candidemia (17.1%) were the main infections. In total, 7 patients (20.0%) died during hospitalization; among them, 6 (17.1%) died within 30 days of diagnosis. CONCLUSIONS: Active screening of exposed patients followed by strict infection control measures, including environmental cleaning, was successful in ending the outbreak. Preventing future outbreaks is challenging due to outside sources of infection and environmental resistance.

Genomic Characterization of Carbapenem-Non-susceptible Pseudomonas aeruginosa Clinical Isolates From Saudi Arabia Revealed a Global Dissemination of GES-5-Producing ST235 and VIM-2-Producing ST233 Sub-Lineages.

Carbapenem-resistant P. aeruginosa has become a major clinical problem due to limited treatment options. However, studies assessing the trends in the molecular epidemiology and mechanisms of antibiotic resistance in this pathogen are lacking in Saudi Arabia. Here, we reported the genome characterization in a global context of carbapenem non-susceptible clinical isolates from a nationally representative survey. The antibiotic resistance profiles of the isolates (n = 635) collected over 14 months between March 2018 and April 2019 from different geographical regions of Saudi Arabia showed resistance rates to relevant ß-lactams, aminoglycosides and quinolones ranging between 6.93 and 27.56%. Overall, 22.52% (143/635) of the isolates exhibited resistance to both imipenem and meropenem that were mainly explained by porin loss and efflux overexpression. However, 18.18% of resistant isolates harbored genes encoding GES (69.23%), VIM (23.07%), NDM (3.85%) or OXA-48-like (3.85%) carbapenemases. Most common GES-positive isolates produced GESs -5, -15 or -1 and all belonged to ST235 whereas the VIM-positive isolates produced mainly VIM-2 and belonged to ST233 or ST257. GES and VIM producers were detected at different sampling periods and in different surveyed regions. Interestingly, a genome-wide comparison revealed that the GES-positive ST235 and VIM-2-positive ST233 genomes sequenced in this study and those available through public databases from various locations worldwide, constituted each a phylogenetically closely related sub-lineage. Profiles of virulence determinants, antimicrobial resistance genes and associated mobile elements confirmed relatedness within each of these two different sub-lineages. Sequence analysis located the bla GES gene in nearly all studied genomes (95.4%) in the same integrative conjugative element that also harbored the acc(6')-Ib, aph(3')-XV, aadA6, sul1, tet(G), and catB resistance genes while bla VIM-2 in most (98.89%) ST233-positive genomes was co-located with aac(6')-I1, dfrB-5, and aac(3')-Id in the same class I integron. The study findings revealed the global spread of GES-5 ST235 and VIM-2 ST233 sub-lineages and highlighted the importance of routine detection of rare ß-lactamases.