Phenotypic and genotypic characterisation of cephalosporin-, carbapenem- and colistin-resistant Gram-negative bacterial pathogens in Lebanon, Jordan and Iraq

Prevalence of bacteremia and antimicrobial resistance pattern among patients in South Lebanon

BACKGROUND

Bacteremia is a leading cause of morbidity and mortality worldwide. Rising prevalence and antimicrobial resistance (AMR) are critical public health issues. This study aims to determine the prevalence of bacteremia and the AMR pattern among patients in South Lebanon.

METHODS

A cross-sectional study analyzed 76 positive blood cultures from Hammoud and Labib Hospitals in South Lebanon between September 2023 and March 2024. The phenotype and antimicrobial susceptibility of gram-positive and gram-negative were determined by using disk diffusion. Genotypically, polymerase chain reaction was used to detect the carbapenemase-resistant Enterobacterales (CRE), extended-spectrum β-lactamases (ESBL), and methicillin-resistant Staphylococcus aureus genes.

RESULTS

Out of 76 isolates, 38 (50%) were gram-positive and 38 (50%) were gram-negative. Escherichia coli was the most common among gram-negative (18. 42%), with 10.52% ESBL and 3.94% CRE. Staphylococcus coagulase negative was the most common among gram-positive (40.78%), followed by Staphylococcus aureus (6.57%), with 3.94% methicillin-resistant S. aureus. The prevalent ESBL gene was CTX-M (100%), and for the CRE, NDM (66.66%) was the most common gene. Regarding S. aureus, 66.66% were mecA.

DISCUSSION

The diverse bacteremia isolates and resistance genes in South Lebanon reflect global variability in incidence and resistance profiles.

CONCLUSIONS

High rates of bacteremia and AMR in South Lebanon underscore the need for effective antibiotic stewardship programs.

Risk factors associated with multidrug-resistant Klebsiella pneumoniae infections: a multicenter observational study in Lebanese hospitals

BACKGROUND

Klebsiella pneumoniae is a significant global public health burden, especially in low-income countries and regions with fragile healthcare infrastructures, due to its ability to cause severe infections, increase mortality rates, and its rising antimicrobial resistance. This study aimed to estimate the proportion of multidrug-resistant (MDR) K. pneumoniae infections and identify associated risk factors.

METHODS

Data were retrospectively collected from three academic hospitals in Beirut, Lebanon, between January 2021 and September 2023 using a standardized form. Binary logistic regression was used to determine risk factors associated with MDR, extended-spectrum beta-lactamase (ESBL)-producing, and carbapenem-resistant K. pneumoniae (CRKP) infections.

RESULTS

Out of 2,655 K. pneumoniae cases, 410 met the inclusion criteria. The primary infection sources were the urinary tract (58.3%) and the respiratory tract (12.4%). Among the isolates, 61% were MDR K. pneumoniae, with 7.3% being extensively drug-resistant, and 0.5% pandrug-resistant. Additionally, 36.8% were ESBL-producing, while 6.3% were CRKP. Predictors significantly associated with MDR K. pneumoniae infections included male sex (adjusted odds ratio [AOR] = 3.46, 95% CI = 1.01-11.86, P = 0.04), recent antibiotics use (AOR = 4.52, 95% CI = 1.65-12.36, P = 0.003), and recent cancer chemotherapy (AOR = 3.43, 95% CI = 1.25-9.42, P = 0.01). ESBL-producing infections were associated with age ≥ 65 years, higher Charlson Comorbidity Index (CCI), and recent antibiotic use. CRKP infections were linked to male sex, prior antibiotic use, and longer hospital stays prior to infection (all P < 0.05).

CONCLUSIONS

MDR K. pneumoniae infections are steadily rising in Lebanon, along with an increase in ESBL-producing and CRKP cases. The main risk factors for MDR K. pneumoniae infections were male sex, recent antibiotic use, and cancer chemotherapy. ESBL-producing infections were associated with advanced age, higher CCI, and recent antibiotic use, while CRKP infections were linked to male sex, prior antibiotic use, and prolonged hospital stays. This situation is further exacerbated by inadequate healthcare infrastructure and suboptimal national surveillance. Strengthening local surveillance and implementing effective antibiotic stewardship programs are critical to managing this growing threat..

Epidemiology and antimicrobial resistance trends of Acinetobacter species in the United Arab Emirates: a retrospective analysis of 12 years of national AMR surveillance data

INTRODUCTION

Acinetobacter spp., in particular A. baumannii, are opportunistic pathogens linked to nosocomial pneumonia (particularly ventilator-associated pneumonia), central-line catheter-associated blood stream infections, meningitis, urinary tract infections, surgical-site infections, and other types of wound infections. A. baumannii is able to acquire or upregulate various resistance determinants, making it frequently multidrug-resistant, and contributing to increased mortality and morbidity. Data on the epidemiology, levels, and trends of antimicrobial resistance of Acinetobacter spp. in clinical settings is scarce in the Gulf Cooperation Council (GCC) and Middle East and North Africa (MENA) regions.

METHODS

A retrospective 12-year analysis of 17,564 non-duplicate diagnostic Acinetobacter spp. isolates from the United Arab Emirates (UAE) was conducted. Data was generated at 317 surveillance sites by routine patient care during 2010-2021, collected by trained personnel and reported by participating surveillance sites to the UAE National AMR Surveillance program. Data analysis was conducted with WHONET.

RESULTS

Species belonging to the A. calcoaceticus-baumannii complex were mostly reported (86.7%). They were most commonly isolated from urine (32.9%), sputum (29.0%), and soft tissue (25.1%). Resistance trends to antibiotics from different classes during the surveillance period showed a decreasing trend. Specifically, there was a significant decrease in resistance to imipenem, meropenem, and amikacin. Resistance was lowest among Acinetobacter species to both colistin and tigecycline. The percentages of multidrug-resistant (MDR) and possibly extensively drug-resistant (XDR) isolates was reduced by almost half between the beginning of the study in 2010 and its culmination in 2021. Carbapenem-resistant Acinetobacter spp. (CRAB) was associated with a higher mortality (RR: 5.7), a higher admission to ICU (RR 3.3), and an increased length of stay (LOS; 13 excess inpatient days per CRAB case), as compared to Carbapenem-susceptible Acinetobacter spp.

CONCLUSION

Carbapenem-resistant Acinetobacter spp. are associated with poorer clinical outcomes, and higher associated costs, as compared to carbapenem-susceptible Acinetobacter spp. A decreasing trend of MDR Acinetobacter spp., as well as resistance to all antibiotic classes under surveillance was observed during 2010 to 2021. Further studies are needed to explore the reasons and underlying factors leading to this remarkable decrease of resistance over time.

Carbapenem resistant Enterobacterales in the United Arab Emirates: a retrospective analysis from 2010 to 2021

BACKGROUND

Carbapenem-resistant Enterobacterales (CRE) are spreading in the United Arab Emirates (UAE) where their dissemination is facilitated by international travel, trade, and tourism. The objective of this study is to describe the longitudinal changes of CRE as reported by the national AMR surveillance system of the UAE.

METHODS

In this study, we retrospectively describe CRE isolated from 317 surveillance sites, including 87 hospitals and 230 centers/clinics from 2010 to 2021. The associated clinical, demographic, and microbiological characteristics are presented by relying on the UAE national AMR surveillance program. Data was analyzed using WHONET microbiology laboratory database software (http://www.whonet.org).

RESULTS

A total of 14,593 carbapenem resistant Enterobacterales were analyzed, of which 48.1% were carbapenem resistant Klebsiella pneumoniae (CRKp), 25.1% carbapenem resistant Escherichia coli (CREc), and 26.8% represented 72 other carbapenem resistant species. Carbapenem resistant strains were mostly associated with adults and isolated from urine samples (36.9% of CRKp and 66.6% of CREc) followed by respiratory samples (26.95% for CRKp) and soft tissue samples (19.5% for CRKp). Over the studied period carbapenem resistance rates remained high, especially in K. pneumoniae, and in 2021 were equivalent to 67.6% for imipenem, 76.2% for meropenem, and 91.6% for ertapenem. Nevertheless, there was a statistically significant decreasing trend for imipenem and meropenem resistance in Klebsiella species (p < 0.01) while the decrease in ertapenem resistance was non-significant. Concerning E. coli, there was a statistically significant decreasing trend for meropenem and imipenem resistance over the 12 years, while ertapenem resistance increased significantly with 83.8% of E. coli exhibiting ertapenem resistance in 2021. Resistance rates to ceftazidime and cefotaxime remained higher than 90% (in 2021) for CRKp and cefotaxime rates increased to 90.5% in 2021 for CREc. Starting 2014, resistance to colistin and tigecycline was observed in carbapenem resistant Enterobacterales. CRE were associated with a higher mortality (RR: 6.3), admission to ICU (RR 3.9), and increased length of stay (LOS; 10 excess inpatient days per CRE case).

CONCLUSION

This study supports the need to monitor CRE in the UAE and draws attention to the significant increase of ertapenem resistance in E. coli. Future surveillance analysis should include a genetic description of carbapenem resistance to provide new strategies.

Acinetobacter baumannii: assessing susceptibility patterns, management practices, and mortality predictors in a tertiary teaching hospital in Lebanon

BACKGROUND

Acinetobacter baumannii is a major nosocomial pathogen capable of causing life-threatening infections. This bacterium is highly resistant to antibiotics and associated with high mortality rates. Therefore, this study aimed to evaluate A. baumannii's susceptibility patterns to antimicrobials, assess the appropriateness of the initiated antimicrobial therapy, determine the mortality rate, and identify predictors associated with mortality.

METHODS

A retrospective observational study was conducted among patients infected with A. baumannii at a university hospital in Lebanon through the revision of medical records. Kaplan-Meier survival analysis and log-rank tests were used to analyze time-to-mortality. Binary logistic regression was performed to identify predictors of mortality.

RESULTS

The records of 188 patients were screened, and 111 patients with A. baumannii infection were enrolled. Almost all isolates were resistant to carbapenem, and 43% of the isolates were extensively-drug resistant. Almost half of the patients received initial inappropriate antimicrobial therapy (n = 50, 45.1%). The 30-day mortality rate associated with A. baumannii infection was 71.2% (79/111). The time to mortality in patients who received inappropriate antimicrobial therapy (5.70 ± 1.07 days) was significantly shorter than in those who received appropriate antimicrobial therapy (12.43 ± 1.01 days, P < 0.01). Binary logistic regression revealed that inappropriate antimicrobial therapy (adjusted odds ratio [AOR] = 16.22, 95% CI 2.68-9.97, P = 0.002), mechanical ventilation (AOR = 14.72, 95% CI 3.27-6.61, P < 0.001), and thrombocytopenia (AOR = 8.82, 95% CI 1.12-9.75, P = 0.003) were more likely associated with mortality.

CONCLUSIONS

A. baumannii exhibits an alarming mortality rate among infected patients. Thrombocytopenia, mechanical ventilation, and inappropriate antibiotic administration are associated with mortality in patients infected with A. baumannii. The prompt initiation of appropriate antimicrobial therapy, infection control measures, and effective stewardship program are crucial to reduce the incidence of A. baumannii and improve the treatment outcomes.

Antimicrobial resistance landscape and COVID-19 impact in Egypt, Iraq, Jordan, and Lebanon: A survey-based study and expert opinion

OBJECTIVES

The objective of this study was to assess the antimicrobial resistance (AMR) landscape and the impact of COVID-19 on AMR in Egypt, Iraq, Jordan, and Lebanon, and to gather expert opinions on the barriers to the implementation of antimicrobial stewardship (AMS) initiatives in the region.

METHODS

A cross-sectional questionnaire survey was used to assess the current AMR landscape, existing AMS initiatives, barriers to implementing AMS initiatives, and the impact of COVID-19 on AMR in the four countries.

RESULTS

The survey was completed by 204 physicians from Egypt (n = 82), Lebanon (n = 49), Iraq (n = 43), and Jordan (n = 30). Previous antibiotic use and previous bacterial colonization were perceived as the most common risk factors for an increase in AMR. According to the survey, multidrug-resistant (MDR) gram-negative bacteria were most common in lower respiratory tract infections, and Klebsiella pneumoniae and Escherichia coli were the most commonly identified gram-negative bacteria in hospital-acquired infections. Only 14.8% of pediatric physicians and 28.6% of adult physicians reported that target pathogen genotyping and phenotyping were done in hospitals, and the most commonly reported reasons for the lack of testing were technological and resource constraints. These constraints, coupled with the scarcity and high cost of newer antibiotics, have been identified as the most significant barriers to the successful management of MDR gram-negative bacterial infections in the region. It was reported that the spectrum of activity and safety of the antibiotic, the site of infection, the presence of comorbidities, and published guidelines and local antibiograms determined the choice of empirical antibiotic therapy for patients in the region. The four countries experienced a significant rise in AMR due to several factors during the COVID-19 pandemic, including an increase in hospital occupancy, a shift in priorities away from AMR surveillance, and changes in AMR epidemiology. Additionally, the large volumes of unnecessary and unsubstantiated antibiotic prescriptions during the COVID-19 pandemic has led to subsequent antibiotic shortages and significant increases in AMR in the region. Physicians also noted that the majority of COVID-19 patients were already on antibiotics before visiting the healthcare facility. MDR gram-negative bacteria were found in the majority of COVID-19 patients admitted to the intensive care unit. Despite the fact that various AMS initiatives have been implemented, they are not standardized across the region. Some of the main barriers to AMS implementation in the region are a lack of adequately trained AMS staff, lack of AMS knowledge and training among healthcare professionals, financial constraints, and the lack of AMR surveillance systems.

CONCLUSION

These survey results provide valuable insights into the existing AMR and AMS landscape in the region, as well as the barriers that impede efficient AMS and AMR management. Based on these findings, the authors developed a call to action that suggests ways for each country in the region to address these challenges.

Emergence of a Hybrid IncI1-Iα Plasmid-Encoded blaCTX-M-101 Conferring Resistance to Cephalosporins in Salmonella enterica Serovar Enteritidis

The increasing resistance to cephalosporins in Salmonella poses a serious threat to public health. In our previous study, the bla_CTX-M-101 gene, a new bla_CTX-M variant, was first reported in Salmonella enterica serovar Enteritidis (S. Enteritidis). Here, we further analyzed the genome characterization, transferability, and resistance mechanism of one S. Enteritidis isolate (SJTUF14523) carrying bla_CTX-M-101 from an outpatient in 2016 in Xinjiang, China. This strain was a multidrug resistance (MDR) isolate and exhibited resistance to ceftazidime (MIC = 64 μg/mL), cefotaxime (MIC = 256 μg/mL), and cefepime (MIC = 16 μg/mL). Phylogenetic analysis revealed that SJTUF14523 had a close relationship to another S. Enteritidis isolate from the United States. In the presence of plasmid p14523A, there were 8- and 2133-fold increases in the MICs of cephalosporins in Escherichia coli C600 in the conjugation. Gene cloning results indicated that bla_CTX-M-101 was the decisive mechanism leading to ceftazidime and cefotaxime resistance that could make the MICs break through the resistance breakpoint. Plasmid sequencing revealed that the bla_CTX-M-101 gene was located on an IncI1-Iα transferable plasmid (p14523A) that was 85,862 bp in length. Sequence comparison showed that p14523A was a novel hybrid plasmid that might have resulted from the interaction between a homologous region. Furthermore, we found a composite transposon unit composed of ISEcp1, bla_CTX-M-101, and orf477 in p14523A. ISEcp1-mediated transposition was likely to play a key role in the horizontal transfer of bla_CTX-M-101 among plasmids in S. Enteritidis. Collectively, these findings underline further challenges in the prevention and control of antibiotic resistance posed by new CTX-M-101-like variants in Salmonella.

Extended Spectrum- and Carbapenemase-Based β-Lactam Resistance in the Arabian Peninsula-A Descriptive Review of Recent Years

Antimicrobial resistance (AMR) is a global problem that also includes countries of the Arabian Peninsula. Of particular concern, is the continuing development of extended-spectrum β-lactamases (ESBLs) in the countries of this region. Additionally, antibiotic treatment options for ESBL-producing bacteria are becoming limited, primarily due to the continuing development of carbapenem resistance (CR), carbapenems being frequently used to treat such infections. An overview of recent publications (2018-2021) indicates the presence of ESBL and/or CR in patients and hospitals in most countries of the Arabian Peninsula, although the delay between microbial isolation and publication inevitably makes an accurate analysis of the current situation rather difficult. However, there appears to be greater emphasis on CR (including combined ESBL and CR) in recent publications. Furthermore, although publications from Saudi Arabia are the most prevalent, this may simply reflect the increased interest in ESBL and CR within the country. Enhanced ESBL/CR surveillance is recommended for all countries in the Arabian Peninsula.