Clinical, phenotypic, and genotypic characteristics of ESBL-producing Salmonella enterica bloodstream infections from Qatar

Background

Resistant Salmonella infections are a major global public health challenge particularly for multidrug-resistant (MDR) isolates manifesting as bloodstream infections (BSIs).

Objectives

To evaluate clinical, phenotypic, and genotypic characteristics of extended-spectrum beta-lactamase (ESBL) producing Salmonella enterica BSIs from Qatar.

Methods

Phenotypic ESBL Salmonella enterica from adult patients presenting with positive BSIs were collected between January 2019 to May 2020. Microbiological identification and characterization were performed using standard methods while genetic characteristics were examined through whole genome sequencing studies.

Results

Of 151 episodes of Salmonella enterica BSI, 15 (10%) phenotypic ESBL isolates were collected. Recent travel was recorded in most cases (80%) with recent exposure to antimicrobials (27%). High-level resistance to quinolines, aminoglycosides, and cephalosporins was recorded (80-100%) while meropenem, tigecycline and colistin demonstrated universal susceptibility. Genomic evaluation demonstrated dominance of serotype Salmonella Typhi sequence type 1 (93%) while antimicrobial resistance genes revealed dominance of aminoglycoside resistance (100%), qnrS1 quinolones resistance (80%), blaCTX-M-15 ESBLs (86.7%), and paucity of AmpC resistance genes (6.7%).

Conclusions

Invasive MDR Salmonella enterica is mainly imported, connected to patients from high prevalent regions with recent travel and antimicrobial use caused by specific resistant clones. In suspected cases of multidrug resistance, carbapenem therapy is recommended.

Streptococcus gordonii-associated infective endocarditis: Case series, literature review, and genetic study

Key Clinical Message

Streptococcus gordonii-associated endocarditis is a rare occurrence, raising diagnostic challenges, and is often associated with considerable morbidity. However, vigilance can prevent devastating consequences.

Abstract

Streptococcus gordonii-associated endocarditis is rarely reported but often associated with considerable morbidity. We describe three cases of infective endocarditis caused by S. gordonii during a four-week period in 2023, and the use of whole-genome sequencing to determine whether these isolates were genetically related. The available literature was reviewed.

Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections

Candida glabrata is a commensal yeast of the gastrointestinal tract and skin of humans. However, it causes opportunistic infections in immunocompromised patients, and is the second most common Candida pathogen causing bloodstream infections. Although there are many studies on the epidemiology of C. glabrata infections, the fine- and large-scale geographical nature of C. glabrata remain incompletely understood. Here we investigated both the fine- and large-scale population structure of C. glabrata through genome sequencing of 80 clinical isolates obtained from six tertiary hospitals in Qatar and by comparing with global collections. Our fine-scale analyses revealed high genetic diversity within the Qatari population of C. glabrata and identified signatures of recombination, inbreeding and clonal expansion within and between hospitals, including evidence for nosocomial transmission among coronavirus disease 2019 (COVID-19) patients. In addition to signatures of recombination at the population level, both MATa and MATα alleles were detected in most hospitals, indicating the potential for sexual reproduction in clinical environments. Comparisons with global samples showed that the Qatari C. glabrata population was very similar to those from other parts of the world, consistent with the significant role of recent anthropogenic activities in shaping its population structure. Genome-wide association studies identified both known and novel genomic variants associated with reduced susceptibilities to fluconazole, 5-flucytosine and echinocandins. Together, our genomic analyses revealed the diversity, transmission patterns and antifungal drug resistance mechanisms of C. glabrata in Qatar as well as the relationships between Qatari isolates and those from other parts of the world.

Molecular characterization of Candida auris outbreak isolates in Qatar from patients with COVID-19 reveals the emergence of isolates resistant to three classes of antifungal drugs

OBJECTIVES

During the COVID-19 pandemic in Qatar, many patients who were severely ill were colonized and infected by Candida auris, an invasive multidrug-resistant yeast pathogen that spreads through nosocomial transmission within healthcare facilities. Here, we investigated the molecular epidemiology of these C. auris isolates and the mechanisms associated with antifungal drug resistance.

METHODS

Whole genomes of 76 clinical C. auris isolates, including 65 from patients with COVID-19 collected from March 2020 to June 2021, from nine major hospitals were sequenced on Illumina NextSeq. Single nucleotide polymorphisms were used to determine their epidemiological patterns and mechanisms for antifungal resistance. The data were compared with those published prior to the COVID-19 pandemic from 2018 to 2020 in Qatar.

RESULTS

Genomic analysis revealed low genetic variability among the isolates from patients with and without COVID-19, confirming a clonal outbreak and ongoing dissemination of C. auris among various healthcare facilities. Based on antifungal susceptibility profiles, more than 70% (22/28) of isolates were resistant to both fluconazole and amphotericin B. Variant analysis revealed the presence of multi-antifungal resistant isolates with prominent amino acid substitutions: Y132F in ERG11 and V704L in CDR1 linked to reduced azole susceptibility and the emergence of echinocandin resistance samples bearing mutations in FKS1 in comparison with pre-COVID-19 pandemic samples. One sample (CAS109) was resistant to three classes of antifungal drugs with a unique premature stop codon in ERG3 and novel mutations in CDR2, which may be associated with elevated amphotericin B and azole resistance.

DISCUSSION

Candida auris isolates from patients with COVID-19 and from most patient samples without COVID-19 in Qatar were highly clonal. The data demonstrated the emergence of multidrug-resistant strains that carry novel mutations linked to enhanced resistance to azoles, echinocandins, and amphotericin B. Understanding the epidemiology and drug resistance will inform the infection control strategy and drug therapy.

1725. National Surveillance of Gram-negative Bacteria in Qatar, the Study for Monitoring of Antimicrobial Resistance Trends (SMART): from 2017 to 2019

Background

Monitoring Antimicrobial Resistance Trends (SMART) is a global study for the surveillance of antimicrobial resistance (AMR) in Gram-negative bacteria (GNB) from different regions around the World including Gulf countries. To evaluate prevalence and trends in AMR in GNB from clinical specimens including microbiological and genomic characteristics as well as examine Antimicrobial Susceptibility Tests (AST) for existing and novel antimicrobials.

Methods

A prospective study was conducted on clinical specimens from Hamad Medical Corporation, Qatar, between 2017 and 2019 according to the SMART protocol that covers community as well as hospital-associated infections reported to secondary care. Consecutive GNB were included from different sites including lower respiratory and urinary tracts, intrabdominal, and bloodstream infections.

Results

Over the three years study period, 895 isolates were studied from the specified sites comprising 38 GNB with four key pathogens: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia. Meropenem resistance was 3.6% for E. coli and 9.3% for K. pneumoniae while imipenem/relebactam resistance was 3% compared to 8% respectively. The overall ceftolozane/tazobactam resistance for E. coli was 9% (25/281) compared to 13% (34/257) for K. pneumoniae while resistance for ceftazidime/avibactam was 2% (3/137) and 4% (5/117) respectively. Genomic characteristics of 70 Enterobacterales including 48 carbapenem-resistant, revealed the prevalence of β-lactamase from all classes dominated by bla_CXM-15 while carbapenem resistance revealed a paucity of bla_KPC and supremacy of bla_OXA-48 like and bla_NDM resistance genes (Table 1). Table 1.

Massilia timonae bacteremia: An unusual pathogen of septic abortion

Massilia timonae infections in humans have rarely been reported. To the best of our knowledge, M. timonae has not been previously recognized as a causative agent of obstetric or gynecological infections. Timely identification of this unusual pathogen and the use of targeted antimicrobial therapy are crucial to avoid consequences and treatment failure.

An enemy in shadows-Mycoplasma hominis septic arthritis and iliopsoas abscess: Case report and review of the literature

Mycoplasma hominis (M. hominis) is fastidious and difficult to grow bacteria with the ability to colonize the genitourinary and respiratory tracts. Infrequently can cause a variety of genitourinary tract infections, pregnancy complications, and neonatal diseases. M. hominis rarely reported to cause extragenital infections and seldomly native joint septic arthritis particularly in immunocompromised hosts, raising diagnostic challenges and is often associated with delayed diagnosis and high morbidity and mortality. We report the case of a 30-year-old patient who developed M. hominis native left hip septic arthritis with iliopsoas abscess after receiving rituximab for newly diagnosed thrombotic thrombocytopenic purpura (TTP). The diagnosis of M. hominis hip septic arthritis with iliopsoas involvement was confirmed following repeated joint and abscess aspiration and identification of the organism with the aid of culture and specific Polymerase chain reaction (PCR). The patient was subsequently treated with a prolonged course of antibiotics targeting the organism with a favorable outcome. The clinical presentations, assessment, and management of this rare entity of M. hominis related extragenital infections are outlined. In addition, the literature on similar cases was reviewed to raise awareness and avoid devastating consequences.

Ominous combination: COVID-19 disease and Candida auris fungemia-Case report and review of the literature

The identification of Candida auris fungemia in critically ill COVID-19 patients is detrimental, with huge implications on patient mortality and infectious control measures.

Central line-associated Rhodotorula mucilaginosa fungemia in an immunocompetent host: Case report and review of the literature

Rhodotorula mucilaginosa is an emerging fungal infection with the ability of biofilms formation. The identification of R mucilaginosa fungemia should trigger reflexes of prompt central venous line removal and using Amphotericin therapy.

Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

One hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). bla_NDM-1 (45; 30.2%) and bla_OXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

Identification of mcr-8 in Clinical Isolates From Qatar and Evaluation of Their Antimicrobial Profiles

This study was performed to investigate the genotypic causes of colistin resistance in 18 colistin-resistant Klebsiella pneumoniae (n = 13), Escherichia coli (n = 3) and Pseudomonas aeruginosa (n = 2) isolates from patients at the Hamad General Hospital, Qatar. MIC testing for colistin was performed using Phoenix (BD Biosciences, Heidelberg, Germany) and then verified with SensiTest Colistin (Liofilchem, Zona Ind. le, Italy). Strains determined to be resistant (MIC > 4-16 μg/mL) were then whole-genome sequenced (MiSeq, Illumina, Inc.). Sequences were processed and analysed using BacPipe v1.2.6, a bacterial whole genome sequencing analysis pipeline. Known chromosomal modifications were determined using CLC Genomics Workbench v.9.5.3 (CLCbio, Denmark). Two K. pneumoniae isolates (KPN-15 and KPN-19) harboured mcr-8.1 on the IncFII(K) plasmids, pqKPN-15 and pqKPN-19, and belonged to ST383 and ST716, respectively. One E. coli isolate harboured mcr-1.1 on the IncI2 plasmid pEC-12. The other 15 isolates harboured known chromosomal mutations linked to colistin resistance in the PhoPQ two-component system. Also, three K. pneumoniae strains (KPN-9, KPN-10 and KPN-15) showed disruptions due to IS elements in mgrB. To our knowledge, this marks the first description of mcr-8.1 in K. pneumoniae of human origin in Qatar. Currently, more research is necessary to trace the source of mcr-8.1 and its variants in humans in this region.

Emergence of Multidrug- and Pandrug- Resistant Pseudomonas aeruginosa from Five Hospitals in Qatar

Background

A global rise in multidrug-resistant (MDR) nosocomial infections has led to a significant increase in morbidity and mortality. MDR Gram-negative bacteria (GNB) are recognised for rapidly developing drug resistance. Despite Pseudomonas aeruginosa being the second most common GNB isolated from healthcare associated infections, the magnitude of MDR P. aeruginosa (MDR-PA) has not been evaluated in Qatar.

Aim

To assess the prevalence and antimicrobial susceptibility patterns of MDR-PA from 5 major hospitals in Qatar.

Methods

A total of 2533 P. aeruginosa clinical isolates were collected over a one-year period. MDR-PA was defined as resistance to at least one agent of ≥ 3 antibiotic classes. Clinical and demographic data were collected prospectively.

Findings

The overall prevalence of MDR-PA isolates was 8.1% (205/2533); the majority of isolates were from patients exposed to antibiotics during 90 days prior to isolation (85.4 %, 177/205), and the infections were mainly hospital-acquired (95.1%, 195/205) with only 4.9% from the community. The majority of MDR-PA isolates were resistant to cefepime (96.6%, 198/205), ciprofloxacin, piperacillin/tazobactam (91%, 186/205), and meropenem (90%, 184/205). Patient comorbidities with MDR-PA were diabetes mellitus (47.3%, n=97), malignancy (17.1%, n=35), end-stage renal disease (13.7%, n=28) and heart failure (10.7%, n=22).

Conclusion

There was a significant prevalence of MDR-PA in Qatar, primarily from healthcare facilities and associated with prior antibiotic treatment. There was an alarming level of antimicrobial resistance to carbapenems. Our results are part of a national surveillance of MDR to establish effective containment plans.