A systematic review of healthcare-associated infections in Africa: An antimicrobial resistance perspective

High prevalence of carbapenem-resistant Enterobacterales (CRE) in human samples from Nigeria: A systematic review and meta-analysis

Objectives

The rise in Carbapenem-resistant Enterobacterales (CRE) is perturbing. To curb the menace of CRE, a comprehensive understanding of its prevalence and epidemiology is crucial. As varying reports abound, the true prevalence of CRE in Nigeria remains unknown. Here, we conducted a systematic review and meta-analysis following standard guidelines to assess the situation of CRE in Nigeria.

Methods

We searched electronic databases including Pubmed, ScienceDirect, Scopus, Web of Science, and Google Scholar for articles providing information on CRE in Nigeria. The data gathered were analyzed using OpenMeta Analyst and Comprehensive Meta-Analysis software. The random-effect model was employed to calculate pooled resistance to carbapenem antibiotics.

Results

From 321 retrieved records, 57 were finally included. The studies were predominantly from the South-West region (n = 19). Escherichia coli and Klebsiella pneumoniae were the most frequently tested Enterobacterales among the included studies. The pooled prevalence estimate for imipenem resistance among CRE was 11.2 % (95 % CI: 7.9-15.7). Meropenem resistance had an estimate of 13.5 % (95 % CI: 9.1-19.6), whereas ertapenem and doripenem were estimated at 17.0 % (95 % CI: 9.9-27.7) and 37.9 % (95 % CI: 15.0-67.8), respectively. High heterogeneity (I 2 >85 %, p < 0.001) was observed for the estimates. The highest resistance rate to imipenem (28.4 %), meropenem (37.2 %) and ertapenem (46.5 %) were observed for the South-South region. Based on specific CRE genera, Morganella sp. was the most resistant (37.0 %) while Escherichia sp. was the least (9.4 %). Our analyses also revealed a progressive increase in resistance to carbapenem antibiotics over the years.

Conclusion

This study highlights carbapenem resistance as a concern in Africa's most populous nation, underscoring the need for proactive measures to address and mitigate the threat of CRE.

Financial and economic costs of healthcare-associated infections in Africa

BACKGROUND

Healthcare-associated infections (HAIs) remain a global health challenge, and have elevated rates in Sub-Saharan Africa. HAIs impact patients and their families by causing illness, prolonged hospital stay, potential disability, excess costs and, sometimes, death. The costs of HAIs are increasing due to spreading antimicrobial resistance. A major risk factor for HAIs is lack of water, sanitation and hygiene (WASH); environmental cleaning and healthcare waste management. In Sub-Saharan Africa, these services are lacking in at least 50% of healthcare facilities.

AIM

To estimate the costs associated with HAIs at national level in 14 countries in Sub-Saharan Africa.

METHODS

Economic methodologies were employed to estimate the medical costs, productivity losses and value of premature death from HAIs, drawing on national statistics and published studies to populate the economic model.

RESULTS

In 2022, the number of HAIs was estimated at 4.8 million, resulting in 500,000 deaths. Health-related economic losses amounted to US$13 billion per year, equivalent to 1.14% of combined gross domestic product and US$15.7 per capita. Healthcare costs were US$500 per HAI, and represented 5.6% of total health expenditure. The costs of providing basic WASH were US$0.91 per capita, which, if they reduced HAIs by 50%, would result in benefit-cost ratios of 1.6 (financial healthcare savings alone) and 8.6 (all economic benefits).

CONCLUSION

HAIs have a major health and economic burden on African societies, and a significant proportion can be prevented. It is critical that health policy makers and practitioners dedicate policy space, resources and training to address HAIs.

Antimicrobial Resistance in the WHO African Region: A Systematic Literature Review 2016-2020

Antimicrobial resistance (AMR) is a significant global public health threat. This review presents the most recent in-depth review of the situation of the main AMR types in relation to the most commonly prescribed antibiotics in the World Health Organization (WHO) African Region. Underlying genes of resistance have been analyzed where possible. A search to capture published research data on AMR from articles published between 2016 and 2020 was done using PubMed and Google Scholar, with rigorous inclusion/exclusion criteria. Out of 48003 articles, only 167 were included. Among the tested gram-negative bacteria species, Klebsiella spp. remain the most tested, and generally the most resistant. The highest overall phenotypic resistance for imipenem was reported in E. coli, whereas for meropenem, E. coli and Haemophilus spp. showed an equal resistance proportion at 2.5%. For gram-positive bacteria, Streptococcus pneumoniae displayed high resistance percentages to trimethoprim/sulfamethoxazole (64.3%), oxacillin (32.2%), penicillin (23.2%), and tetracycline (28.3%), whereas Staphylococcus aureus contributed to 22.8% and 10% resistance to penicillin and oxacillin, respectively. This review shows that AMR remains a major public health threat. The present findings will help public health decision-makers in developing efficient preventive strategies and adequate policies for antibiotic stewardship and surveillance in line with the global action plan for AMR.

Whole-Genome Analysis of Extensively Drug-Resistant Enterobacter hormaechei Isolated from a Patient with Non-Hodgkin's Lymphoma

BACKGROUND

Currently, the Enterobacteriaceae species are responsible for a variety of serious infections and are already considered a global public health problem, especially in underdeveloped countries, where surveillance and monitoring programs are still scarce and limited. Analyses were performed on the complete genome of an extensively antibiotic-resistant strain of Enterobater hormaechei, which was isolated from a patient with non-Hodgkin's lymphoma, who had been admitted to a hospital in the city of Manaus, Brazil.

METHODS

Phenotypical identification and susceptibility tests were performed in automated equipment. Total DNA extraction was performed using the PureLink genomic DNA mini-Kit. The genomic DNA library was prepared with Illumina Microbial Amplicon Prep and sequenced in the MiSeq Illumina Platform. The assembly of the whole-genome and individual analyses of specific resistance genes extracted were carried out using online tools and the Geneious Prime software.

RESULTS

The analyses identified an extensively resistant ST90 clone of E. hormaechei carrying different genes, including blaCTX-M-15, blaGES-2, blaTEM-1A, blaACT-15, blaOXA-1 and blaNDM-1, [aac(3)-IIa, aac(6')-Ian, ant(2″)-Ia], [aac(6')-Ib-cr, (qnrB1)], dfrA25, sul1 and sul2, catB3, fosA, and qnrB, in addition to resistance to chlorhexidine, which is widely used in patient antisepsis.

CONCLUSIONS

These findings highlight the need for actions to control and monitor these pathogens in the hospital environment.

Effectiveness of infection prevention and control interventions in health care facilities in Africa: A systematic review

BACKGROUND

Health care-associated infections (HAIs) are a major threat to patient safety and quality care. However, they are avoidable by implementing evidence-based infection prevention and control (IPC) measures. This review evaluated the evidence of the effectiveness of IPC interventions in reducing rates of HAIs in health care settings in Africa.

METHODS

We searched several databases: CENTRAL, EMBASE, PUBMED, CINAHL, WHO IRIS, and AJOL for primary studies reporting rates of the 4 most frequent HAIs: surgical site infections, central line--associated bloodstream infections, catheter-associated urinary tract infections, ventilator-associated pneumoniae, and increase in hand hygiene compliance. Two reviewers appraised the studies and PRISMA guidelines were followed.

RESULTS

Out of 4,624 studies identified from databases and additional sources, 15 studies were finally included in the review. The majority of studies were of pre- and post-test study design. All the studies implemented a combination of interventions and not as stand-alone components. Across all included studies, an improvement was reported in at least 1 primary outcome.

CONCLUSIONS

Our review highlights the potential of IPC interventions in reducing HAIs and improving compliance with hand hygiene in health care facilities in Africa. For future research, we recommend more pragmatic study designs with improved methodological rigor.

Adherence to Infection Prevention Practice Standard Protocol and Associated Factors Among Healthcare Workers

Introduction

Healthcare-associated infection affects more than 100 million patients annually. Healthcare workers' poor adherence to standard infection prevention and control procedures can result in many negative consequences, ranging from disability to death.

Methods

A facility-based, cross-sectional study was conducted in June 2021 among 379 healthcare workers selected using a stratified random sampling technique. All types of healthcare providers except pharmacy professionals were included in the study. Standardization and validation of the study tool were performed ahead of data collection. Multivariable regression was used to assess the variables associated with adherence.

Results

The study found that 60.2% of healthcare workers (95% CI, 55.1-65.2) had good adherence to infection prevention practices, and 68.7% and good knowledge of infection prevention practices. Training on infection prevention methods (adjusted odds ratio [AOR] = 1.68; 95% CI, 1.04-2.72), availability of water supply at hand washing station (AOR = 2.90; 95% CI, 1.62-5.31), and attitude toward infection prevention (AOR = 2.64; 95% CI, 1.65-4.24) were identified as predictors of adherence to infection prevention and control procedures.

Conclusion

More than half of the participants had good adherence to infection prevention guideline practices. In-service infection prevention training, a consistent water supply at the hand washing station, and a positive attitude of participants were associated with good adherence to infection prevention practices.

Healthcare-Associated Infections in a Tertiary Care Hospital: Significance of Patient Referral Practices

Introduction

Nosocomial infections, also known as healthcare-associated infections (HCAIs), are infections that a patient acquires while receiving healthcare services within 48 hours of admission to hospital. In high income countries, an average of 7% of hospitalised patients acquire a nosocomial infection. In low and middle income countries, however, prevalence rates can be as high as 30%. This is due to limited resources and supplies for infection control, inadequate training and lack of compliance with infection prevention and control regulations.

Methods

A cross-sectional, hospital based study was conducted among patients admitted to a tertiary care facility in Tanzania. A semi-structured questionnaire was used to collect information from 134 patients in different wards. Correlation and multivariate regression analyses were performed to determine the association between the independent variables, i.e. chronic illness, invasive procedures, use of antibiotics and referral status, and the dependent variable, i.e. new symptom, and their level of significance. The significance level was set at P≤ .05.

Results

A total of 134 patients participated in the study. Of the total number, 61% (n=82) of the patients were male and 43% (n=57) were referrals from other institutions. Fifteen percent (n=21) of the surveyed patients reported a new symptom. There was a positive correlation between referral status and invasive procedure with the occurrence of a new symptom. Multivariate analysis identified 'referral status' as an independent significant factor positively associated with healthcare-associated infetions (P=.041).

Conclusions

The results indicate a prevalence of 15.7% of healthcare-associated infections, which is unacceptably high for a tertiary care facility. Referral status was independently and significantly associated with HCAI. Improving patient referral patterns and hospital infection control can significantly reduce the risk of healthcare-associated infections.

Antimicrobial Resistance Patterns in Patients with Vaginal Discharge: A 2019-2022 Analysis at the National Health Laboratory in Eritrea

Background

Antimicrobial resistance poses a significant global threat to the treatment of bacterial infections, particularly in low- and middle-income regions such as Africa. This study is aimed at analyzing antimicrobial resistance patterns in vaginal swab samples from patients at the National Health Laboratory from 2019 to 2022.

Methods

This retrospective study examined patient records from vaginal swab analyses performed at the National Health Laboratory between January 1, 2019, and December 31, 2022. Ethical approval was obtained from the Ministry of Health Research Ethical Approval and Clearance Committee on 15/02/2023.

Results

Of the 622 samples, 83% underwent microbial isolation and identification. Citrobacter spp. exhibited high resistance (>43%) to antibiotics such as cephalexin, ceftazidime, nalidixic acid, ampicillin, gentamicin, and tetracycline. E. coli showed resistance rates of more than 50% to ampicillin, trimethoprim-sulfamethoxazole, and tetracycline. Klebsiella spp. and Proteus spp. exhibited resistance rates that exceeded 47% to specific antibiotics. Gram-positive bacteria have resistance rates of more than 49% with ampicillin, trimethoprim-sulfamethoxazole, tetracycline, oxacillin, vancomycin, and penicillin G. In particular, S. aureus demonstrated no resistance to rifampicin or clindamycin, while Streptococcus spp. showed 100% resistance to rifampicin and vancomycin. Several species, including Proteus species, Streptococcus spp., S. aureus, and Klebsiella spp. exhibited multidrug resistance.

Conclusion

Most gram-negative bacteria displayed higher resistance of >45% to ampicillin, trimethoprim-sulfamethoxazole, and tetracycline. Among gram-positive bacteria, a higher resistance rate with ampicillin, trimethoprim-sulfamethoxazole, tetracycline, oxacillin, vancomycin, and penicillin G was recorded. S. aureus showed no resistance to rifampicin and clindamycin, and Strep. spp. indicated 100% resistance to rifampicin and vancomycin. This study highlights critical gaps and areas for further exploration. Expanding the spectrum of antibiotics tested and investigating underlying multidrug resistance mechanisms would provide a more comprehensive understanding of resistance patterns.

Knowledge, practice and associated factors towards intravenous cannula-related infection prevention among nurses working at Northwest Amhara Regional State Comprehensive Specialized Hospitals, Ethiopia

BACKGROUND

Intravenous cannula-related infections are one of the leading causes of healthcare-associated infections. It leads to morbidity and mortality in hospitalized patients. Nurses play a significant role in the prevention of these infections. Whereas in Ethiopia, there is limited information and published studies done on nurses' knowledge, practice, and associated factors and also most of other available studies done only the magnitude it lack associated factors. The purpose of this study was to assess nurses' knowledge, practice, and associated factors toward intravenous cannula-related infection prevention.

METHODS

An institution-based cross-sectional study was conducted at Northwest Amhara Regional State Comprehensive Specialized Hospitals on May 1-30/2022. By using single population proportion formula the sample size was determined; we used a 50% proportion value (0.05), and 95% Confidence Interval 5% margin of error. A simple random sampling method was used to select 423 nurses. The data were collected by using structured pretested self-administered questionnaires. Then coded, and enter into epi-data version 4.6 and exported into the statistical package for social science version 23 for cleaning and analyzing the data. Data were presented by texts, tables, and figures. A binary logistic regression model was used to assess the association between variables. Based on the adjusted odds ratio, variables having a p-value less than 0.05 with a 95% confidence interval were used to state associated with the outcome variables.

RESULTS

A total of 412 nurses participated in this study with 97.4% response rate. The participants had good knowledge and practice in proportions of (54. 9%) and (53. 4%) respectively. Being male, working wards/units, having training, and a higher educational level were factors that were significantly associated to having good knowledge. Working wards/units, having good knowledge, training, and access to guidelines were significantly associated with performing good practice.

CONCLUSION

The finding of this study revealed that nearly half of the nurses had poor knowledge and practice in intravenous cannula-related infection prevention. As a result, hospital administrators and other concerned stakeholders better to prepare and ensure that guidelines are available, provide training, and develop the educational levels of nurses.

Prevalence, risk factors, and antimicrobial resistance of endemic healthcare-associated infections in Africa: a systematic review and meta-analysis

BACKGROUND

Healthcare-associated infections (HCAI) place a significant burden on healthcare systems globally. This systematic review and meta-analysis aimed to investigate the prevalence, risk factors, and aetiologic agents of endemic HCAI in Africa.

METHODS

MEDLINE/PubMed, CINAHL, and Global Health databases (EBSCOhost interface) were searched for studies published in English and French describing HCAI in Africa from 2010 to 2022. We extracted data on prevalence of HCAI, risk factors, aetiologic agents, and associated antimicrobial resistance patterns. We used random-effects models to estimate parameter values with 95% confidence intervals for risk factors associated with HCAI. This study was registered in PROSPERO (CRD42022374559) and followed PRISMA 2020 guidelines.

RESULTS

Of 2541 records screened, 92 were included, comprising data from 81,968 patients. Prevalence of HCAI varied between 1.6 and 90.2% with a median of 15% across studies. Heterogeneity (I2) varied from 93 to 99%. Contaminated wound (OR: 1.75, 95% CI: 1.31-2.19), long hospital stay (OR: 1.39, 95% CI: 0.92-1.80), urinary catheter (OR: 1.57, 95% CI: 0.35-2.78), intubation and ventilation (OR: 1.53, 95% CI: 0.85-2.22), vascular catheters (OR: 1.49, 95% CI: 0.52-2.45) were among risk factors associated with HCAI. Bacteria reported from included studies comprised 6463 isolates, with E. coli (18.3%, n = 1182), S. aureus (17.3%, n = 1118), Klebsiella spp. (17.2%, n = 1115), Pseudomonas spp. (10.3%, n = 671), and Acinetobacter spp. (6.8%, n = 438) being most common. Resistance to multiple antibiotics was common; 70.3% (IQR: 50-100) of Enterobacterales were 3rd -generation cephalosporin resistant, 70.5% (IQR: 58.8-80.3) of S. aureus were methicillin resistant and 55% (IQR: 27.3-81.3) Pseudomonas spp. were resistant to all agents tested.

CONCLUSIONS

HCAI is a greater problem in Africa than other regions, however, there remains a paucity of data to guide local action. There is a clear need to develop and validate sustainable HCAI definitions in Africa to support the implementation of routine HCAI surveillance and inform implementation of context appropriate infection prevention and control strategies.

Epidemiology, risk factors, and clinical outcomes of carbapenem-resistant Enterobacterales in Africa: A systematic review

OBJECTIVES

Carbapenem-resistant Enterobacterales (CRE) commonly cause hospital-acquired infections and hospital outbreaks worldwide, with an alarming increase in Africa, necessitating review of regional CRE epidemiological trends.

METHODS

A systematic review was conducted using PRISMA guidelines, searching PubMed, Scopus and Web of Science databases for studies describing CRE distribution, risk factors for CRE acquisition and clinical outcome of CRE infections in Africa.

RESULTS

One-hundred and sixty-nine studies were included, with the majority from North Africa (92/169, 54.4%). Most studies (136/169; 80.4%) focused only on infection, with a total of 15666 CRE isolates (97.4% clinical infection, 2.6% colonisation). The leading bacterial species included Klebsiella (72.2%), Escherichia coli (13.5%), and Enterobacter (8.3%). The most frequently detected carbapenemases were NDM (43.1%) and OXA-48-like (42.9%). Sequence types were reported in 44 studies, with ST101 and ST147 most commonly reported in K. pneumoniae, and ST410, ST167 and ST38 in E. coli. Previous antibiotic use, prior hospitalisation, surgical procedures, indwelling devices, intensive care unit admission and prolonged hospital stay, were the most frequent factors associated with CRE infection/colonisation. Crude mortality for CRE infection was 37%.

CONCLUSION

Although K. pneumoniae and E. coli remain the most frequent CRE in Africa, observed sequence types are not the commonly reported global 'high-risk' clones. The distribution of species and carbapenemases differs across African regions, while risk factors for CRE colonisation/infection, and patient outcomes are similar to those reported globally. There are limited data on CREs from parts of Africa, highlighting the need to strengthen epidemiologic surveillance programmes in the region.

The burden of hospital acquired infections and antimicrobial resistance

The burden of Hospital care-associated infections (HCAIs) is becoming a global concern. This is compounded by the emergence of virulent and high-risk bacterial strains such as "ESKAPE" pathogens - (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), especially within Intensive care units (ICUs) that house high-risk and immunocompromised patients. In this review, we discuss the contributions of AMR pathogens to the increasing burden of HCAIs and provide insights into AMR mechanisms, with a particular focus on last-resort antibiotics like polymyxins. We extensively discuss how structural modifications of surface-membrane lipopolysaccharides and cationic interactions influence and inform AMR, and subsequent severity of HCAIs. We highlight some bacterial phenotypic survival mechanisms against polymyxins. Lastly, we discuss the emergence of plasmid-mediated resistance as a phenomenon making mitigation of AMR difficult, especially within the ICUs. This review provides a balanced perspective on the burden of HCAIs, associated pathogens, implication of AMR and factors influencing emerging AMR mechanisms.

Drug resistance and extended-spectrum β-lactamase (ESBLs) - producing Enterobacteriaceae, Acinetobacter and Pseudomonas species from the views of one-health approach in Ethiopia: a systematic review and meta-analysis

BACKGROUND

Although antimicrobial resistance (AMR) bacteria present a significant and ongoing public health challenge, its magnitude remains poorly understood, especially in many parts of the developing countries. Hence, this review was conducted to describe the current pooled prevalence of drug resistance, multidrug- resistance (MDR), and Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, Acinetobacter, and Pseudomonas species in humans, the environment, and animals or food of animal origin in Ethiopia.

METHODS

PubMed, Google Scholar, and other sources were searched for relevant articles as per the preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines. A critical appraisal for screening, eligibility, and inclusion in the meta-analysis was made based on the Joanna Briggs Institute's (JBI) essential appraisal tools. The meta-analysis was done on Statistical Software Package (STATA) version 17.0.

RESULTS

A total of 33 research articles were included in this systematic review and meta-analysis. Escherichia coli, Klebsiella species, Acinetobacter, and Pseudomonas species were the most frequently reported bacteria from two or more sources. More than 50% of Klebsiella species and 25% to 89% of Escherichia coli from two or more sources were resistant to all analysed antibiotics, except carbapenems. Fifty-five percent (55%) to 84% of Acinetobacter species and 33% to 79% of Pseudomonas species from human and environmental sources were resistant to all analyzed antibiotics. Carbapenem resistance was common in Acinetobacter and Pseudomonas species (38% to 64%) but uncommon in Enterobacteriaceae (19% to 44%). Acinetobacter species (92%), Klebsiella species (86%), and Pseudomonas species (79%) from human sources, and Proteus species (92%), and Acinetobacter species (83%), from environmental sources, were the common multidrug-resistant isolates. About 45% to 67% of E. coli, Klebsiella, Acinetobacter, and Pseudomonas species from human and environmental sources were ESBL producers.

CONCLUSION

Our review report concluded that there was a significant pooled prevalence of drug resistance, MDR, and ESBL-producing Enterobacteriaceae, Acinetobacter, and Pseudomonas species from two or more sources. Hence, our finding underlines the need for the implementation of integrated intervention approaches to address the gaps in reducing the emergence and spread of antibiotic- resistant bacteria.

Investigating the evolution and predicting the future outlook of antimicrobial resistance in sub-saharan Africa using phenotypic data for Klebsiella pneumoniae: a 12-year analysis

BACKGROUND

Antimicrobial resistance (AMR) is a major public health challenge, particularly in sub-Saharan Africa (SSA). This study aimed to investigate the evolution and predict the future outlook of AMR in SSA over a 12-year period. By analysing the trends and patterns of AMR, the study sought to enhance our understanding of this pressing issue in the region and provide valuable insights for effective interventions and control measures to mitigate the impact of AMR on public health in SSA.

RESULTS

The study found that general medicine patients had the highest proportion of samples with AMR. Different types of samples showed varying levels of AMR. Across the studied locations, the highest resistance was consistently observed against ceftaroline (ranging from 68 to 84%), while the lowest resistance was consistently observed against ceftazidime avibactam, imipenem, meropenem, and meropenem vaborbactam (ranging from 92 to 93%). Notably, the predictive analysis showed a significant increasing trend in resistance to amoxicillin-clavulanate, cefepime, ceftazidime, ceftaroline, imipenem, meropenem, piperacillin-tazobactam, and aztreonam over time.

CONCLUSIONS

These findings suggest the need for coordinated efforts and interventions to control and prevent the spread of AMR in SSA. Targeted surveillance based on local resistance patterns, sample types, and patient populations is crucial for effective monitoring and control of AMR. The study also highlights the urgent need for action, including judicious use of antibiotics and the development of alternative treatment options to combat the growing problem of AMR in SSA.

Antimicrobial Resistance Patterns and Risk Factors Associated with ESBL-Producing and MDR Escherichia coli in Hospital and Environmental Settings in Lusaka, Zambia: Implications for One Health, Antimicrobial Stewardship and Surveillance Systems

Antimicrobial resistance (AMR) is a public health problem threatening human, animal, and environmental safety. This study assessed the AMR profiles and risk factors associated with Escherichia coli in hospital and environmental settings in Lusaka, Zambia. This cross-sectional study was conducted from April 2022 to August 2022 using 980 samples collected from clinical and environmental settings. Antimicrobial susceptibility testing was conducted using BD PhoenixTM 100. The data were analysed using SPSS version 26.0. Of the 980 samples, 51% were from environmental sources. Overall, 64.5% of the samples tested positive for E. coli, of which 52.5% were from clinical sources. Additionally, 31.8% were ESBL, of which 70.1% were clinical isolates. Of the 632 isolates, 48.3% were MDR. Most clinical isolates were resistant to ampicillin (83.4%), sulfamethoxazole/trimethoprim (73.8%), and ciprofloxacin (65.7%) while all environmental isolates were resistant to sulfamethoxazole/trimethoprim (100%) and some were resistant to levofloxacin (30.6%). The drivers of MDR in the tested isolates included pus (AOR = 4.6, CI: 1.9-11.3), male sex (AOR = 2.1, CI: 1.2-3.9), and water (AOR = 2.6, CI: 1.2-5.8). This study found that E. coli isolates were resistant to common antibiotics used in humans. The presence of MDR isolates is a public health concern and calls for vigorous infection prevention measures and surveillance to reduce AMR and its burdens.

Review and analysis of the overlapping threats of carbapenem and polymyxin resistant E. coli and Klebsiella in Africa

BACKGROUND

Carbapenem-resistant Enterobacterales are among the most serious antimicrobial resistance (AMR) threats. Emerging resistance to polymyxins raises the specter of untreatable infections. These resistant organisms have spread globally but, as indicated in WHO reports, the surveillance needed to identify and track them is insufficient, particularly in less resourced countries. This study employs comprehensive search strategies with data extraction, meta-analysis and mapping to help address gaps in the understanding of the risks of carbapenem and polymyxin resistance in the nations of Africa.

METHODS

Three comprehensive Boolean searches were constructed and utilized to query scientific and medical databases as well as grey literature sources through the end of 2019. Search results were screened to exclude irrelevant results and remaining studies were examined for relevant information regarding carbapenem and/or polymyxin(s) susceptibility and/or resistance amongst E. coli and Klebsiella isolates from humans. Such data and study characteristics were extracted and coded, and the resulting data was analyzed and geographically mapped.

RESULTS

Our analysis yielded 1341 reports documenting carbapenem resistance in 40 of 54 nations. Resistance among E. coli was estimated as high (> 5%) in 3, moderate (1-5%) in 8 and low (< 1%) in 14 nations with at least 100 representative isolates from 2010 to 2019, while present in 9 others with insufficient isolates to support estimates. Carbapenem resistance was generally higher among Klebsiella: high in 10 nations, moderate in 6, low in 6, and present in 11 with insufficient isolates for estimates. While much less information was available concerning polymyxins, we found 341 reports from 33 of 54 nations, documenting resistance in 23. Resistance among E. coli was high in 2 nations, moderate in 1 and low in 6, while present in 10 with insufficient isolates for estimates. Among Klebsiella, resistance was low in 8 nations and present in 8 with insufficient isolates for estimates. The most widespread associated genotypes were, for carbapenems, blaOXA-48, blaNDM-1 and blaOXA-181 and, for polymyxins, mcr-1, mgrB, and phoPQ/pmrAB. Overlapping carbapenem and polymyxin resistance was documented in 23 nations.

CONCLUSIONS

While numerous data gaps remain, these data show that significant carbapenem resistance is widespread in Africa and polymyxin resistance is also widely distributed, indicating the need to support robust AMR surveillance, antimicrobial stewardship and infection control in a manner that also addresses broader animal and environmental health dimensions.

Environmental contamination across multiple hospital departments with multidrug-resistant bacteria pose an elevated risk of healthcare-associated infections in Kenyan hospitals

BACKGROUND

Healthcare-associated infections (HAIs) are often caused by multidrug-resistant (MDR) bacteria contaminating hospital environments which can cause outbreaks as well as sporadic transmission.

METHODS

This study systematically sampled and utilized standard bacteriological culture methods to determine the numbers and types of MDR Enterococcus faecalis/faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species, and Escherichia coli (ESKAPEE) from high-touch environments of five Kenyan hospitals; level 6 and 5 hospitals (A, B, and C), and level 4 hospitals (D and E), in 2018. Six hundred and seventeen high-touch surfaces across six hospital departments; surgical, general, maternity, newborn, outpatient and pediatric were sampled.

RESULTS

78/617 (12.6%) of the sampled high-touch surfaces were contaminated with MDR ESKAPEE; A. baumannii, 23/617 (3.7%), K. pneumoniae, 22/617 (3.6%), Enterobacter species, 19/617 (3.1%), methicillin resistant S. aureus (MRSA), 5/617 (0.8%), E. coli, 5/617 (0.8%), P. aeruginosa, 2/617 (0.3%), and E. faecalis and faecium, 2/617 (0.3%). Items found in patient areas, such as beddings, newborn incubators, baby cots, and sinks were the most frequently contaminated. Level 6 and 5 hospitals, B, 21/122 (17.2%), A, 21/122 (17.2%), and C, 18/136 (13.2%), were more frequently contaminated with MDR ESKAPEE than level 4 hospitals; D, 6/101 (5.9%), and E, 8/131 (6.1%). All the sampled hospital departments were contaminated with MDR ESKAPEE, with high levels observed in newborn, surgical and maternity. All the A. baumannii, Enterobacter species, and K. pneumoniae isolates were non-susceptible to piperacillin, ceftriaxone and cefepime. 22/23 (95.6%) of the A. baumannii isolates were non-susceptible to meropenem. In addition, 5 K. pneumoniae isolates were resistant to all the antibiotics tested except for colistin.

CONCLUSION

The presence of MDR ESKAPEE across all the hospitals demonstrated gaps in infection prevention practices (IPCs) that should be addressed. Non-susceptibility to last-line antibiotics such as meropenem threatens the ability to treat infections.

A systematic review and meta-analysis of risk factors associated with healthcare-associated infections among hospitalised patients in Chinese general hospitals from 2001 to 2022

BACKGROUND

Healthcare-associated infections (HAIs) are a serious global public health issue. However, a comprehensive analysis of risk factors for HAIs has yet been undertaken at a large scale among general hospitals in China. The aim of this review is to assess risk factors associated with HAIs in Chinese general hospitals.

METHODS

Medline, EMBASE and Chinese Journals Online databases were searched to find studies published from January 1^st 2001 to May 31^st 2022. The random-effects model was used to estimate odds ratio (OR). Heterogeneity was assessed based on the τˆ² and I² statistics.

RESULTS

5,037 published papers were identified from the initial search and 58 studies were included in the quantitative meta-analysis. 1,211,117 hospitalised patients were incorporated covering 41 regions in 23 provinces of China and 29,737 were identified as having HAIs. Our review showed that HAIs were significantly associated with sociodemographic characteristics including age older than 60 years (OR: 1.74[1.38-2.19]) and male sex (1.33[1.20-1.47]); invasive procedures (3.54[1.50-8.34]); health conditions such as chronic diseases (1.49[1.22-1.82]), coma (OR: 5.12[1.70-15.38]) and immunosuppression (2.45[1.55-3.87]). Other risk factors included long-term bed (5.84[5.12-6.66]), and healthcare-related risk factors as chemotherapy (1.96[1.28-3.01]), haemodialysis (3.12[1.80-5.39]), hormone therapy (2.96[1.96-4.45]), immunosuppression (2.45[1.55-3.87]) and use of antibiotics (6.64 [3.16-13.96]), and longer than 15 hospitalisation days (13.36[6.80-26.26]).

CONCLUSIONS

Being male and aged over 60 years, invasive procedure, health conditions, healthcare-related risk factors, and longer than 15 hospitalisation days were the main risk factors associated with HAIs in Chinese general hospitals. This supports the evidence base to inform the relevant cost effective prevention and control strategies.

Healthcare-associated infections in Africa: a systematic review and meta-analysis of point prevalence studies

BACKGROUND

There is limited data to describe the point-prevalence of healthcare-associated infections (HAIs) among patients at a regional level in Africa. This study estimated the pooled prevalence of HAIs and described the distribution of HAIs as well as the pathogens identified from African studies.

METHODS

PubMed, Scopus and Google Scholar databases were searched to find point-prevalence studies of HAIs in Africa. Studies conducted in Humans that reported the prevalence of HAIs among hospitalized patients and published in English language from January 2010 to March 2022 were selected. Longitudinal studies of HAIs and unpublished studies were excluded. The reference list of the selected studies was checked to find additional studies. A meta-analysis was conducted using RevMan 5.4 and the pooled prevalence of HAIs was determined using a random effect model.

RESULTS

Of the 6094 articles identified from the databases, fifteen eligible articles were selected. The studies were conducted in the North, South, East and West African regions with Tunisia (n = 4) and South Africa (n = 2) having the highest number of studies. Most of the studies (n = 12, 80.0%) had good quality. The pooled prevalence of HAIs was 12.76% (95% confidence interval [CI] 10.30-15.23) with a high degree of heterogeneity (I² = 90.0%). The prevalence of HAIs varied between wards with the highest rate found in the ICU (25.2%-100%), followed by neonatal ICU/ward (7.0%-53.6%) and paediatric medical ward (2.7%-33.0%). Surgical site infection was the most common HAIs and accounted for 41.6% of all HAIs (95% CI 23.55-59.80), followed by bloodstream infection (17.07%, 95% CI 11.80-22.33) and respiratory tract infections/pneumonia (17.04%, 95% CI 13.21-20.87). Recent hospitalization (adjusted odds ratio [AOR]: 4.17, 95% CI 1.85-9.41), presence of peripheral vascular catheter (AOR: 2.87, 95% CI 1.54-5.36) and having diabetes mellitus (AOR: 2.46, 95% CI 1.45-4.17) were the strongest predictors of HAIs in Africa. Only 37.9% of HAIs had documented positive microbiological culture result with gram negative bacteria including Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii and Citrobacter been the most common microorganisms and accounted for 40%-100% of the pathogens.

CONCLUSIONS

The pooled point-prevalence of HAIs in Africa is more than two times higher than the rate reported in developed countries. The prevalence varied between the countries and was highest in the ICU and neonatal ICU/ward. Surgical site infection and bloodstream infection were the most common HAIs reported in African studies. Recent hospitalization, presence of peripheral vascular catheter and having diabetes mellitus were the strongest predictors of HAIs in African studies. Most of the HAIs are preventable with appropriate infection control measures and antimicrobial stewardship. Additional studies are needed especially in the Central African region. Future studies should be designed using standardized protocol and standardized definition to reduce heterogeneity among the studies.

Phage display for the detection, analysis, disinfection, and prevention of Staphylococcus aureus

The World Health Organization has designated Staphylococcus aureus as a global health concern. This designation stems from the emergence of multiple drug-resistant strains that already account for hundreds of thousands of deaths globally. The development of novel treatment strategies to eradicate S. aureus or mitigate its pathogenic potential is desperately needed. In the effort to develop emerging strategies to combat S. aureus, phage display is uniquely positioned to assist in this endeavor. Leveraging bacteriophages, phage display enables researchers to better understand interactions between proteins and their antagonists. In doing so, researchers have the capacity to design novel inhibitors, biosensors, disinfectants, and immune modulators that can target specific S. aureus strains. In this review, we highlight how phage display can be leveraged to design novel solutions to combat S. aureus. We further discuss existing uses of phage display as a detection, intervention, and prevention platform against S. aureus and provide outlooks on how this technology can be optimized for future applications.

Antibiotics use evaluation among hospitalized adult patients at Jimma Medical Center, southwestern Ethiopia: the way to pave for antimicrobial stewardship

BACKGROUND

An irrational antibiotic use is a common problem in developing countries like Ethiopia, which makes empiric antibiotics use difficult. It is considered to be the greatest health problem in our time and future unless intervened. Therefore, this study aimed to assess the patterns of antibiotics use among hospitalized adult patients to pave the way for antimicrobial stewardship.

METHODS

A hospital-based prospective observational study was conducted at Jimma Medical Center, southwestern Ethiopia, from 30 October 2020 to 29 January 2021 with 360 adult hospitalized patients participating. A semi-structured questionnaire and consecutive sampling technique was used for data collection. The data were collected through medical record reviews and patient interviews. The collected data were entered into Epi-data and exported to SPSS® version 23.0 for analysis. Days of therapy (DOT) and essential medicine lists "Access, Watch, and Reserve (AWaRe)" antibiotics classification were used to assess antibiotic use pattern among participants.

RESULTS

The majority of study participants were females (55.3%), attended formal education (59.4%), and live in rural areas (61.4%) with mean age ± (SD) of 37.65 ± (16.75). The overall rate of antibiotics consumption during the study was 111 days of therapy per 100 bed-days and about two-thirds (66%) of the prescribed antibiotics were from the "Watch" group antibiotics. The indicator level of antibiotics use for "Access" group antibiotics was 34% in this study based on the World Health Organization Essential Medicine List. Cephalosporins were the most commonly used class of antibiotics (93.9%).

CONCLUSION

Higher antibiotics exposure and their consumption frequently observed among adult hospitalized patients in the study setting. There was a rapid increase in "Watch" group antibiotics use and about two-thirds of the prescribed antibiotics were from this group. The third-generation cephalosporin were the most commonly used class of antibiotics. Generally, higher consumption and inappropriate antibiotics use among hospitalized adult patients showed the need for urgent interventions by implementing Antimicrobial Stewardship Programs in hospitals.

Activity of ceftolozane/tazobactam against clinical isolates of Pseudomonas aeruginosa from patients in the Middle East and Africa - Study for Monitoring Antimicrobial Resistance Trends (SMART) 2017-2020

OBJECTIVES

We evaluated the activity of ceftolozane/tazobactam (C/T), and comparators against clinical Pseudomonas aeruginosa isolates collected for the global Study for Monitoring Antimicrobial Resistance Trends (SMART) surveillance program in ten countries in the Middle East and Africa to augment scarce standardized surveillance data in this region.

METHODS

Minimum inhibitory concentrations (MICs) were determined using Clinical and Laboratory Standards Institute broth microdilution and interpreted with European Committee on Antimicrobial Susceptibility Testing breakpoints. P. aeruginosa isolates testing with C/T MIC >4 mg/l or imipenem MIC >2 mg/l were screened for β-lactamase genes.

RESULTS

C/T was active against 91.4% and 87.0% of P. aeruginosa isolates from the Middle East and Africa, respectively (14-21 and 7-16 percentage points higher than most β-lactam comparators, respectively). Considerable variation in susceptibility was seen across countries, which largely correlated with the observed prevalence of carbapenemases and/or extended-spectrum β-lactamases. Differences across countries were smaller for C/T than for the β-lactam comparators, ranging from 81% C/T-susceptible among isolates from Jordan to 95% for Qatar. Among subsets resistant to meropenem, ceftazidime, or piperacillin/tazobactam, C/T maintained activity against 51-73% of isolates from the Middle East and against 27-54% from Africa (where metallo-β-lactamase and GES carbapenemase rates were higher).

CONCLUSION

Given the desirability of β-lactam use among clinicians, C/T represents an important option in the treatment of infections caused by P. aeruginosa.

Restoring non-COVID-19 clinical research and surveillance in Oyo state, Nigeria during the SARS-CoV-2pandemic

Background

Many sub-Saharan African patients receive clinical care from extramurally-supported research and surveillance. Dur- ing the COVID-19 pandemic, pausing these activities reduces pa- tient care, surveillance, and research staff employment, increasing pandemic losses. In Oyo State, Nigeria, we paused a multi-country invasive salmonellosis surveillance initiative and a rural clinical bac- teriology project.

Objective

Working with research partners raises health facility con- cerns about SARS-CoV-2 transmission risks and incurs infection pre- vention costs, so we developed and implemented re-opening plans to protect staff and patients and help health facilities deliver care.

Methods

Our reopening plan included appointing safety and per- sonal protective equipment (PPE) managers from existing project staff cadres, writing new standard operating procedures, implement- ing extensive assessed training, COVID-19 testing for staff, procuring and managing PPE, and providing secondary bacteraemia blood culture support for COVID-19 patients in State isolation facilities.

Results

Surveillance data showed that the pandemic reduced care access and negatively affected patient unsupervised antibacterial use. The re-opening plan repurposed human and material resources from national and international extramurally-supported programs to mitigate these effects on public health.

Conclusions

A structured reopening plan restarted care, surveil- lance, and infection prevention and control.

Tackling antimicrobial resistance across sub-Saharan Africa: current challenges and implications for the future

INTRODUCTION

Antimicrobial resistance (AMR) is a concern as this increases morbidity, mortality, and costs, with sub-Saharan Africa having the highest rates globally. Concerns with rising AMR have resulted in international, Pan-African, and country activities including the development of national action plans (NAPs). However, there is variable implementation across Africa with key challenges persisting.

AREAS COVERED

Consequently, there is an urgent need to document current NAP activities and challenges across sub-Saharan Africa to provide future guidance. This builds on a narrative review of the literature.

EXPERT OPINION

All surveyed sub-Saharan African countries have developed their NAPs; however, there is variable implementation. Countries including Botswana and Namibia are yet to officially launch their NAPs with Eswatini only recently launching its NAP. Cameroon is further ahead with its NAP than these countries; though there are concerns with implementation. South Africa appears to have made the greatest strides with implementing its NAP including regular monitoring of activities and instigation of antimicrobial stewardship programs. Key challenges remain across Africa. These include available personnel, expertise, capacity, and resources to undertake agreed NAP activities including active surveillance, lack of focal points to drive NAPs, and competing demands and priorities including among donors. These challenges are being addressed, with further co-ordinated efforts needed to reduce AMR.

National action plan on antimicrobial resistance: An evaluation of implementation in the World Health Organization Africa region

In line with global instruments, within the last five years, two-thirds of all countries in the WHO Africa Region (WHO AFR) have developed a National Action Plan (NAP) on Antimicrobial Resistance (AMR). We sought to evaluate progress made across the countries implementing NAP for effective response to AMR. A semi-structured survey tool was administered to obtain information from national focal persons on the implementation of strategic elements of NAP on AMR. This was followed by a Lessons Learnt Workshop in June 2019 at Douala, Cameroon, where focal persons made presentations on the country’s progress. Later, a desktop review of the LLW report and other key documents was conducted. Countries in WHO AFR that have set up a national surveillance system and are enrolled into the WHO global antimicrobial resistance surveillance system have progressively increased to 30 (of 47 countries), of which 15 are already submitting surveillance data. Of the 20 countries at the Lessons Learnt Workshop, 14 have infection prevention and control (IPC) policies and functional healthcare facility IPC programs, 15 participate in the commemoration of the annual world hand hygiene days. Although almost all countries surveyed have national standard treatment guidelines, only five have incorporated the WHO AWaRe classification into the national essential medicines list. Fourteen of 20 countries have established an active/functional national secretariat/coordinating center for AMR. Discernible progress is being made on the implementation of NAP in WHO AFR region. Gaps identified in the strategic elements of action plans need to be filled for effective AMR control.

Risk of community- and hospital-acquired bacteremia and profile of antibiotic resistance in children hospitalized with severe acute malnutrition in Niger

OBJECTIVE

To estimate the prevalence and antibiotic resistance profile of community- and hospital-acquired bacteremia among hospitalized children with severe acute malnutrition in Niger.

METHODS

A descriptive, longitudinal study was conducted in an intensive nutritional rehabilitation center in Madarounfa, Niger. Children aged 6 to 59 months admitted for inpatient treatment of complicated severe acute malnutrition (n=2187) had blood specimens drawn at admission to assess prevalence of community-acquired bacteremia. Subsequent specimens were drawn per physician discretion to assess incidence of hospital-acquired bacteremia. Antibiotic susceptibility testing was performed on positive blood cultures.

RESULTS

The prevalence of community-acquired bacteremia at admission was at least 9.1% (95% confidence interval [CI]: 8.1, 10.4%), with non-typhoid Salmonella identified in over half (57.8%) of cases. The cumulative incidence of hospital-acquired bacteremia was estimated at 1.2% (95% CI: 0.8, 1.7%), among which the most common organisms were Klebsiella pneumoniae (19.4%), Acinetobacter baumannii (16.1%), Enterococcus faecalis (12.9%), and Escherichia coli (12.9%). In community-acquired bacteremia, 58% cases were resistant to amoxicillin-clavulanate; 100% of hospital-acquired bacteremia cases were resistant to amoxicillin and amoxicillin-clavulanate. Mortality risk was elevated among children with hospital-acquired bacteremia (risk ratio [RR] = 9.32) and community-acquired bacteremia (RR = 2.67).

CONCLUSION

Bacteremia was a significant contributor to mortality. Antibiotic resistance poses a challenge to effective clinical management of severe acute malnutrition.

A systematic review and meta-analysis of disease burden of healthcare-associated infections in China: an economic burden perspective from general hospitals

BACKGROUND

Healthcare-associated infections (HAIs) are a global public health issue. However, the economic burden attributable to HAIs at a national level is unknown in China. The aim of this systematic review was to estimate the direct economic burden caused by HAIs in China.

METHODS

Medline, EMBASE and Chinese Journals Online databases were searched, including studies published from 2009 to 2019. The pooled estimates with 95% Confidential Interval were calculated with Quantile Estimation. The random effect model of the DerSimonian-Laird method was used. The statistical significance was set as P<0.05.

RESULTS

2,756 publications were identified; 6 studies were included in a meta-analysis to calculate the pooled estimates of direct economic burden, while 5 were included in the pooled estimates of the additional economic burden. The pooled median estimates of the total medical expenditure, the medicine expenditure and hospitalisation days per inpatient of patients with HAIs were ¥34,415.62, ¥20,065.21 and 34.01 days, respectively (P <0.0001). The pooled median estimates of the differences of the total medical expenditure, the medicine expenditure and hospitalisation days per inpatient between patients with HAIs and patients without HAIs were ¥24,881.37, ¥9,438.46 and 13.89 days, respectively (P < 0.01).

CONCLUSIONS

The cost of care for patients with HAIs was significantly higher than that for those without HAIs. This excess economic burden is likely to impact on patients and their families as well as health service providers and the health care system as a whole. Effective surveillance systems and cost-effective interventions are needed to control HAIs.

Nosocomial infections in an Iranian educational hospital: an evaluation study of the Iranian nosocomial infection surveillance system

Background

Nosocomial infection (NI) or cross-infection is a major health problem in hospitals worldwide.

Aim

This study aimed to report the status of NIs and to evaluate the Iranian nosocomial infection surveillance system (INISS) in a teaching hospital in the south of Iran.

Methods

This is a comparative historical study on the records of hospital admitted patients from 2018 to 2019. Data on patients who were diagnosed with NI was extracted from the INISS database. The database includes data on the incidence of different types of NIs in each hospital ward, the patient’s infection outcome, the agents involved, and the site of infection.

Results

The results indicated that the rate of NI (cases of NI/ 100 admissions) in the hospital was %2.95. The highest rate of NIs was reported from ICUs. Of the infected patients, 45.61% were female, 98.95% had underlying diseases, and 30.88% died due to nosocomial infections. The median (IQR) of the duration of hospital stay among infected patients was 13 (7–18). The most common site of infection was VAE (ventilator-associated events) (39.40%) and the most common isolated agent, irrespective of the organ involved, was Acinetobacter (spp.) (22.75%).

Conclusions

We reported ICU and Acinetobacter (spp.) as the most affected ward and most common agent involved in recorded NIs respectively. The rate of NI in the study hospital was exceptionally low when compared to its counterparts in a few other developed countries. The INISS needs to be further evaluated with regard to the completeness and representativeness of the surveillance system. Also, we need to evaluate the adherence to the INISS guidelines among staff and physicians in reporting the NIs.

Clones and Clusters of Antimicrobial-Resistant Klebsiella From Southwestern Nigeria

BACKGROUND

Klebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about Klebsiella lineages circulating in Nigeria.

METHODS

We performed whole-genome sequencing (WGS) of 141 Klebsiella isolated between 2016 and 2018 from clinical specimens at 3 antimicrobial-resistance (AMR) sentinel surveillance tertiary hospitals in southwestern Nigeria. We conducted in silico multilocus sequence typing; AMR gene, virulence gene, plasmid, and K and O loci profiling; as well as phylogenetic analyses, using publicly available tools and Nextflow pipelines.

RESULTS

Phylogenetic analysis revealed that the majority of the 134 K. pneumoniae and 5 K. quasipneumoniae isolates from Nigeria characterized are closely related to globally disseminated multidrug-resistant clones. Of the 39 K. pneumoniae sequence types (STs) identified, the most common were ST307 (15%), ST5241 (12%), ST15 (~9%), and ST25 (~6%). ST5241, 1 of 10 novel STs detected, is a single locus variant of ST636 carrying dfrA14, tetD, qnrS, and oqxAB resistance genes. The extended-spectrum β-lactamase (ESBL) gene blaCTX_M-15 was seen in 72% of K. pneumoniae genomes, while 8% encoded a carbapenemase. No isolate carried a combination of carbapenemase-producing genes. Four likely outbreak clusters from 1 facility, within STs 17, 25, 307, and 5241, were ESBL but not carbapenemase-bearing clones.

CONCLUSIONS

This study uncovered known and novel K. pneumoniae lineages circulating in 3 hospitals in Southwest Nigeria that include multidrug-resistant ESBL producers. Carbapenemase-producing isolates remain uncommon. WGS retrospectively identified outbreak clusters, pointing to the value of genomic approaches in AMR surveillance for improving infection prevention and control in Nigerian hospitals.

Reducing the Healthcare-Associated Infections in a Rehabilitation Hospital under the Guidance of Lean Six Sigma and DMAIC

The reduction of healthcare-associated infections (HAIs) is one of the most important issues in the healthcare context for every type of hospital. In three operational units of the Scientific Clinical Institutes Maugeri SpA SB, a rehabilitation hospital in Cassano delle Murge (Italy), some corrective measures were introduced in 2017 to reduce the occurrence of HAIs. Lean Six Sigma was used together with the Define, Measure, Analyze, Improve, Control (DMAIC) roadmap to analyze both the impact of such measures on HAIs and the length of hospital stay (LOS) in the Rehabilitative Cardiology, Rehabilitative Neurology, Functional Recovery and Rehabilitation units in the Medical Center for Intensive Rehabilitation. The data of 2415 patients were analyzed, considering the phases both before and after the introduction of the measures. The hospital experienced a LOS reduction in both patients with and without HAIs; in particular, Cardiology had the greatest reduction for patients with infections (-7 days). The overall decrease in HAIs in the hospital was 3.44%, going from 169 to 121 cases of infections. The noteworthy decrease in LOS implies an increase in admissions and in the turnover indicator of the hospital, which has a positive impact on the hospital management as well as on costs.

Profiles of microorganisms isolated from neonates' blood cultures, incubators, cradles, ventilators, washbasins, and health-workers of Libreville University Hospital Neonatal Service: focus on infection prevention and control measures

Background

Nosocomial infection outbreaks in neonatal services are a serious healthcare concern in both developed and developing countries, but few studies have been conducted in sub-Saharan Africa.

Objective

This study explored the etiology of septicemia in neonates and associated patterns of antimicrobial susceptibility in Gabon.

Methods

We analyzed cultures from neonates’ blood and swabs from medical personnel and equipment located in the neonatology service.

Results

Sixty-eight microorganisms were isolated from the medical personnel and equipment; 46 microorganisms were isolated from neonates’ blood culture. Klebsiella pneumoniae spp pneumoniae was the most common bacteria found in both (30.6% and 26.9%, respectively). All Klebsiella pneumoniae spp pneumonia isolates were resistant to amoxicillin with clavulanic acid, gentamycin resistance ranged from 93% to 100%, and cephalosporin resistance ranged from 33.3% to 47%.

Conclusions:

Awareness of the etiology, prevalence, and outcome of nosocomial infection is the first and most important step to appropriate interventions.

Strategies to Improve Antimicrobial Utilization with a Special Focus on Developing Countries

Antimicrobial resistance (AMR) is a high priority across countries as it increases morbidity, mortality and costs. Concerns with AMR have resulted in multiple initiatives internationally, nationally and regionally to enhance appropriate antibiotic utilization across sectors to reduce AMR, with the overuse of antibiotics exacerbated by the COVID-19 pandemic. Effectively tackling AMR is crucial for all countries. Principally a narrative review of ongoing activities across sectors was undertaken to improve antimicrobial use and address issues with vaccines including COVID-19. Point prevalence surveys have been successful in hospitals to identify areas for quality improvement programs, principally centering on antimicrobial stewardship programs. These include reducing prolonged antibiotic use to prevent surgical site infections. Multiple activities centering on education have been successful in reducing inappropriate prescribing and dispensing of antimicrobials in ambulatory care for essentially viral infections such as acute respiratory infections. It is imperative to develop new quality indicators for ambulatory care given current concerns, and instigate programs with clear public health messaging to reduce misinformation, essential for pandemics. Regular access to effective treatments is needed to reduce resistance to treatments for HIV, malaria and tuberculosis. Key stakeholder groups can instigate multiple initiatives to reduce AMR. These need to be followed up.

Identifying global research gaps to mitigate antimicrobial resistance: A scoping review

OBJECTIVE

Identify research gaps relevant to the global effort to combat antimicrobial resistance.

METHODS

Web of Science, PubMed, Scopus, and Ovid MEDLINE were searched for reviews on antimicrobial resistance published between January 1, 2015 and December 31, 2019. Recommendations for future research were identified.

FINDINGS

Seventy-four reviews met inclusion criteria; 300 research gaps and recommendations were identified. The largest number were from the human health sector (105; 35%) followed by environmental health (72; 23%), animal health (66; 22%), food and feed (14; 5%), and plants and crops (8; 3%); 35 (12%) involved more than one sector. The largest number of gaps concerned surveillance of resistance (68; 23%), followed by study design or methodology (52; 17%), interventions (41; 14%), risk assessment and modeling (35; 12%), ecological (26; 9%) and biochemical (28; 9%) aspects of resistance, interface between reservoirs of resistant pathogens (24; 8%), and economic (15; 5%) and awareness- and behavior-related (11; 4%) aspects of antimicrobial resistance.

CONCLUSIONS

Important research gaps remain in our complete understanding of antimicrobial resistance, and more research is needed about its development, transmission, and impact across the interface of human, animal, and environmental reservoirs.

Increasing Antimicrobial Resistance in Surgical Wards at Mulago National Referral Hospital, Uganda, from 2014 to 2018-Cause for Concern?

Antimicrobial Resistance (AMR) and Healthcare Associated Infections (HAIs) are major global public health challenges in our time. This study provides a broader and updated overview of AMR trends in surgical wards of Mulago National Referral Hospital (MNRH) between 2014 and 2018. Laboratory data on the antimicrobial susceptibility profiles of bacterial isolates from 428 patient samples were available. The most common samples were as follows: tracheal aspirates (36.5%), pus swabs (28.0%), and blood (20.6%). Klebsiella (21.7%), Acinetobacter (17.5%), and Staphylococcus species (12.4%) were the most common isolates. The resistance patterns for different antimicrobials were: penicillins (40-100%), cephalosporins (30-100%), β-lactamase inhibitor combinations (70-100%), carbapenems (10-100%), polymyxin E (0-7%), aminoglycosides (50-100%), sulphonamides (80-100%), fluoroquinolones (40-70%), macrolides (40-100%), lincosamides (10-45%), phenicols (40-70%), nitrofurans (0-25%), and glycopeptide (0-20%). This study demonstrated a sustained increase in resistance among the most commonly used antibiotics in Uganda over the five-year study period. It implies ongoing hospital-based monitoring and surveillance of AMR patterns are needed to inform antibiotic prescribing, and to contribute to national and global AMR profiles. It also suggests continued emphasis on infection prevention and control practices (IPC), including antibiotic stewardship. Ultimately, laboratory capacity for timely bacteriological culture and sensitivity testing will provide a rational choice of antibiotics for HAI.

Novel chromosomal insertions of ISEcp1-blaCTX-M-15 and diverse antimicrobial resistance genes in Zambian clinical isolates of Enterobacter cloacae and Escherichia coli

Background

The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types. bla_CTX-M genes, encoding CTX-M-type ESBLs, are usually found on plasmids, but chromosomal location is becoming common. Given that bla_CTX-M-harboring strains often exhibit multidrug resistance (MDR), it is important to investigate the association between chromosomally integrated bla_CTX-M and the presence of additional antimicrobial resistance (AMR) genes, and to identify other relevant genetic elements.

Methods

A total of 46 clinical isolates of cefotaxime-resistant Enterobacteriaceae (1 Enterobacter cloacae, 9 Klebsiella pneumoniae, and 36 Escherichia coli) from Zambia were subjected to whole-genome sequencing (WGS) using MiSeq and MinION. By reconstructing nearly complete genomes, bla_CTX-M genes were categorized as either chromosomal or plasmid-borne.

Results

WGS-based genotyping identified 58 AMR genes, including four bla_CTX-M alleles (i.e., bla_CTX-M-14, bla_CTX-M-15, bla_CTX-M-27, and bla_CTX-M-55). Hierarchical clustering using selected phenotypic and genotypic characteristics suggested clonal dissemination of bla_CTX-M genes. Out of 45 bla_CTX-M gene-carrying strains, 7 harbored the gene in their chromosome. In one E. cloacae and three E. coli strains, chromosomal bla_CTX-M-15 was located on insertions longer than 10 kb. These insertions were bounded by ISEcp1 at one end, exhibited a high degree of nucleotide sequence homology with previously reported plasmids, and carried multiple AMR genes that corresponded with phenotypic AMR profiles.

Conclusion

Our study revealed the co-occurrence of ISEcp1-bla_CTX-M-15 and multiple AMR genes on chromosomal insertions in E. cloacae and E. coli, suggesting that ISEcp1 may be responsible for the transposition of diverse AMR genes from plasmids to chromosomes. Stable retention of such insertions in chromosomes may facilitate the successful propagation of MDR clones among these Enterobacteriaceae species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-021-00941-8.

A point prevalence survey of antimicrobial utilisation patterns and quality indices amongst hospitals in South Africa; findings and implications

Objectives: Antimicrobial use is growing, driven mainly by rising demands in developing countries. Knowing how antimicrobials are prescribed is important. Consequently, we undertook a point prevalence survey (PPS) quantifying antimicrobial consumption among 18 public sector hospitals across South Africa.Method: A purpose-built web-based application was used to collect PPS data.Results: Out of 4407 adult patients surveyed, 33.6% were treated with an antimicrobial. The most frequently prescribed groups were a combination of penicillins including β-lactamase inhibitors. Amoxicillin combined with an enzyme inhibitor accounted for 21.4% total DDDs. In the medical and surgical wards, Access antimicrobials (54.1%) were mostly used, while in the ICU, Watch antimicrobials (51.5%) were mostly used. Compliance with the South African Standard Treatment Guidelines and Essential Medicines List was 90.2%; however, concerns with extended use of antimicrobials for surgical prophylaxis (73.2% of patients).Conclusion: The web-based PPS tool was easy to use and successful in capturing PPS data since the results were comparable to other PPS studies across Africa. High use of amoxicillin combined with an enzyme inhibitor, possibly because it was among the broad-spectrum antimicrobials in the Access group. The findings will assist with future targets to improve antimicrobial prescribing among public sector hospitals in South Africa.

Healthcare-associated outbreaks of bacterial infections in Africa, 2009-2018: A review

BACKGROUND

Healthcare-associated infections (HAIs) are a major global public health problem, increasing the transmission of drug-resistant infections. In Africa, the prevalence of HAIs among all hospital inpatients is estimated to be between 3% and 15%, but outbreaks are infrequently reported. Failure to detect and/or report outbreaks can increase the risk of ongoing infections and recurrent outbreaks.

METHODS

A search of the PubMed, Web of Science, Cochrane Library, and other outbreak databases was performed to identify published literature on bacterial HAI outbreaks in Africa (January 2009 to December 2018). Details of the outbreak characteristics, hospital environment, and the control measures implemented were extracted.

RESULTS

Twenty-two studies published over the 10-year period were identified. These reported 31 distinct outbreaks and a total of 31 causative pathogens, including Klebsiella pneumoniae (six outbreaks, 19%), Staphylococcus aureus (six outbreaks, 19%), and Enterococcus (five outbreaks, 16%). Most outbreaks were reported from university (n = 8, 26%) and tertiary hospitals (n = 11, 55%), from South Africa (n = 9, 41%) and Tunisia (n = 4, 18%). Interventions to control the outbreaks were described in 27 (90%) outbreaks, and all instituted or recommended enhancing hand hygiene and education.

CONCLUSIONS

Few facilities in Africa reported HAI outbreaks over the 10-year period, suggesting substantial under-detection and under-reporting. The quality and timeliness of reporting require improvement to ensure changes in public health practice.

Incidence and risk factors for hospital-acquired infection among paediatric patients in a teaching hospital: a prospective study in southeast Ethiopia

OBJECTIVES

In order to maximise the prevention of hospital-acquired infections (HAIs) and antimicrobial resistance, data on the incidence of HAIs are crucial. In Ethiopia, data about the occurrence of HAIs among hospitalised paediatric patients are lacking. We aim to determine the incidence and risk factors of HAIs among paediatric patients in Ethiopia.

DESIGN

A prospective cohort study.

SETTING

A teaching hospital in southeast Ethiopia.

PARTICIPANTS

448 hospitalised paediatric patients admitted between 1 November 2018 and 30 June 2019.

PRIMARY AND SECONDARY OUTCOME MEASURES

Incidence and risk factors of hospital-acquired infections.

RESULTS

A total of 448 paediatric patients were followed for 3227 patient days. The median age of the patients was 8 months (IQR: 2-26 months). The incidence rate of HAIs was 17.7 per 1000 paediatric days of follow-up; while the overall cumulative incidence was 12.7% (95% CI 9.8% to 15.8%) over 8 months. Children who stayed greater than 6 days in the hospital (median day) (adjusted risk ratio (RR): 2.58, 95% CI 1.52 to 4.38), and children with underlying disease conditions of severe acute malnutrition (adjusted RR: 2.83, 95% CI 1.61 to 4.97) had higher risks of developing HAIs.

CONCLUSIONS

The overall cumulative incidence of HAIs was about 13 per 100 admitted children. Length of stay in the hospital and underlying conditions of severe acute malnutrition were found to be important factors associated with increased risk of HAIs.

Strategies to Prevent Healthcare-Associated Infections: A Narrative Overview

Healthcare-associated infections (HCAIs) are a major source of morbidity and mortality and are the second most prevalent cause of death. Furthermore, it has been reported that for every one-hundred patients admitted to hospital, seven patients in high-income economies and ten in emerging and low-income economies acquire at least one type of HCAI. Currently, almost all pathogenic microorganisms have developed antimicrobial resistance, and few new antimicrobials are being developed and brought to market. The literature search for this narrative review was performed by searching bibliographic databases (including Google Scholar and PubMed) using the search terms: "Strategies," "Prevention," and "Healthcare-Associated Infections," followed by snowballing references cited by critical articles. We found that although hand hygiene is a centuries-old concept, it is still the primary strategy used around the world to prevent HCAIs. It forms one of a bundle of approaches used to clean and maintain a safe hospital environment and to stop the transmission of contagious and infectious microorganisms, including multidrug-resistant microbes. Finally, antibiotic stewardship also has a crucial role in reducing the impact of HCAIs through conserving currently available antimicrobials.

Antibiotic resistance and sensitivity pattern of Metallo-β-Lactamase Producing Gram-Negative Bacilli in ventilator-associated pneumonia in the intensive care unit of a public medical school hospital in Bangladesh

BACKGROUND

Ventilator-associated pneumonia (VAP) is the most common nosocomial infection in intensive care units (ICU), accounting for 25% of all ICU infections. Antimicrobial resistance is increasing and becoming a significant health problem worldwide, increasing hospital length of stay, mortality and costs. Identifying antibiotic resistance patterns in VAP is important as this can cause outbreaks in ICUs. To date, there have been limited studies assessing this in Bangladesh. Consequently, the primary objective of this research was to study the species of bacterial growth and to determine the antibiotic resistance patterns of Metallo-β-Lactamase (MBL) producing gram-negative bacilli among ICU patients with VAP in a public medical school hospital, Bangladesh. In addition, identify the factors associated with a positive culture to provide future guidance.

METHOD

Cross-sectional study performed in the Chattogram Medical College Hospital, Bangladesh. Mueller Hinton agar plates were used for antibiotic sensitivity testing by the Kirby-Buer disc diffusion test.

RESULTS

Among 105 clinically suspected VAP cases, qualitative cultures were positive in 95 (90%) of them. The most common bacteria identified were Acinetobacter spp. (43.2%), Klebsiella spp. (20%) and Pseudomonas spp. (18.9%). A positive culture was not associated with patients' age or gender. Among 41 isolated Acinetobacter spp., 38 (92.7%) were resistant to gentamicin followed by 36 (87.8%) to ceftriaxone. Among 24 isolated Klebsiella spp., 22 (83.3%) were resistant to ceftriaxone. Among 18 isolated Pseudomonas spp., 16 (88.8%) were resistant to ciprofloxacin, and 13 (72.2%) were resistant to ceftriaxone. Among nine isolated E. coli, all were resistant to ceftriaxone and ciprofloxacin. All four Proteus spp. (100%) isolated were resistant to ciprofloxacin. Additionally, phenotype MBL producing was 65.22% and genotype was 45.65% among imipenem resistant pathogens. Imipenem resistant pathogens were sensitive to amoxyclav, amikacin¸ azithromycin, ceftazidime, ceftriaxone, colistin and gentamycin.

CONCLUSION

A positive culture was detected in 90% of VAP patients, but it was not associated with the patients' age and gender. The most common bacteria identified were Acinetobacter spp., Klebsiella spp. and Pseudomonas spp., where the majority of these were resistant to ceftriaxone. The results are being used to provide future guidance on the empiric management of VAP in this hospital.

Bacteriological Study of Electronic Devices Used by Healthcare Workers at Ruhengeri Referral Hospital

Electronic devices have become one of the most essential accessories being used in hospitals. Those devices increase the communication and contact making healthcare delivery more efficient and quality service oriented. The study was designed to collect reliable information about the spreading of pathogens through electronic devices especially in sensitive departments. The objectives of this study were to evaluate the bacterial colonization of electronic devices and determine the effectiveness of disinfection with alcohol 70% (w/v) to reduce the bacterial colonization of electronic devices. It was a cross-sectional study where samples were collected by means of moistened swabs in sterile saline solution from 30 electronic devices used by healthcare workers at Ruhengeri Referral Hospital within four different units: maternity, neonathology, intensive care, and theater room. To evaluate the effects of disinfection using 70% isopropyl alcohol, the second sample collection was carried out after decontamination with 70% isopropyl alcohol. Samples were analyzed in the microbiology lab of INES-Ruhengeri. The result showed that Staphylococcus aureus was the most predominant with 22.5%. Lactobacillus and Citrobacter spp. were 12.5%; Pseudomonas aeruginosa, coagulase-negative Staphylococci, and Serratia marcescens were 10%; Escherichia coli was 7.5%; Klebsiella spp. and Providencia spp. were at 5%. The lowest prevalence was 2.5% of Enterobacter spp. and Salmonella spp. The threat of dissemination of isolated microorganisms is valid, since all devices evaluated in this study showed bacterial contamination of species associated to hospital-acquired infections. Special care should be taken when using electronic devices in healthcare settings in addition to disinfection to reduce the risk of transmission of bacterial agents. Further studies should evaluate the antibiotic susceptibility for better conclusive results since all isolated bacteria in this study were subjected to high resistance and were associated with nosocomial infections.

Knowledge and attitudes towards antibiotic use and resistance among undergraduate healthcare students at University of Rwanda

Background

Antimicrobial resistance (AMR) is an imminent threat to modern medicine. As the efficacy of treatment regimens is reduced, mortality and morbidity attributed to infectious diseases is expected to rise dramatically across the globe. Antimicrobial stewardship and good prescription practices are critical to conserving available therapeutics; it is appropriate, therefore, to appraise our attitudes and knowledge of antimicrobial resistance, particularly for the future healthcare practitioners.

Methods

This is a descriptive cross-sectional study that was conducted among 282 medicals, dental and pharmacy students from the University of Rwanda. Questionnaires were used to collect data from the 4th to 29th March 2017.

Results

Students from Level 3 to level 6 have demonstrated a good knowledge on antibiotics and antimicrobial resistance. Generally, 95% (n = 218) agreed that the inappropriate use of antibiotics could lead to antibiotic resistance. It was found that 96% (n = 220) of the respondents had heard about AMR outside their degree courses. 49% (n = 112) of the participants reported that they are able to purchase antibiotics without a prescription. 96% (n = 220) agreed that it was important for healthcare students to be knowledgeable about antimicrobial resistance. Perhaps most surprisingly, it was found that 83% (n = 191) of participants were unfamiliar with the concept of antimicrobial stewardship and 49% (n = 21) had not yet discussed antimicrobial resistance as part of their education, albeit only 1% (n = 3) was completely unfamiliar with the term. Furthermore, 38% (n = 86) did not support that the antibiotics were overused in Rwanda, 23% (n = 10) did not agree that inappropriate antimicrobial use contributed to antimicrobial resistance, and 50% (n = 22) of participants agreed that antibiotics were indicated in the treatment of pain and inflammation.

Conclusions

The present study reports a moderate knowledge on AMR among the healthcare students. The gaps in the current formal training of healthcare individuals have been identified as well. We highlight the necessity to enhance educational approaches to introduce the key concepts of AMR and antimicrobial stewardship to the curriculum of healthcare students.

High contribution and impact of resistant gram negative pathogens causing surgical site infections at a multi-hospital healthcare system in Saudi Arabia, 2007-2016

Background

Despite being largely preventable, surgical site infections (SSIs) are still one of the most frequent healthcare-associated infections. The presence of resistant pathogens can further augment their clinical and economic impacts. The objective was to estimate the distribution and resistance in SSI pathogens in Saudi Arabia and to compare them to the US National Healthcare Safety Network (NHSN) hospitals.

Methods

Targeted SSI surveillance was prospectively conducted on several surgical procedures done between 2007 and 2016 in four hospitals of Ministry of National Guard Health Affairs. Definitions and methodology of SSI and bacterial resistance were based on NHSN.

Results

A total 492 pathogens causing 403 SSI events were included. The most frequent pathogens were Staphylococcus aureus (22.8%), Pseudomonas aeruginosa (20.1%), Klebsiella spp. (12.2%), and Escherichia coli (12.2%), with marked variability between surgeries. Approximately 30.3% of Staphylococcus aureus was methicillin-resistant (MRSA), 13.0% of Enterococcus spp. was vancomycin-resistant (VRE), and 5.5% of Enterobacteriaceae were carbapenem resistant (CRE). The highest multidrug-resistant (MDR) GNPs were Acinetobacter spp. (58.3%), Klebsiella spp. (20.4%) and Escherichia coli (16.3%). MRSA was significantly less frequent while cephalosporin-resistant Klebsiella spp., MDR Klebsiella spp., and MDR Escherichia coli were significantly more frequent in our hospitals compared with NHSN hospitals.

Conclusion

GNPs in a tertiary care setting in Saudi Arabia are responsible for more than 60% of SSI with more resistant patterns than Western countries. This information may be critical to secure resources and ensure support for caregivers and healthcare leaders in implementing antimicrobial stewardship programs and evidence-based SSI preventive practices.

Direct medical burden of antimicrobial-resistant healthcare-associated infections: empirical evidence from China

BACKGROUND

Antimicrobial resistance (AMR) and healthcare-associated infections (HAIs) are among the biggest global public health challenges, and overlap widely. These infections cause significant morbidity and mortality, put pressure on health systems, and incur rising direct and indirect costs.

AIM

This study analysed the direct medical burden attributable to AMR-HAIs in Chinese public tertiary hospitals, and aimed to inform both the medical regulators and hospital managers for better control of HAIs and containment of AMR.

METHODS

The propensity score matching method (γ= 0.25σ, nearest neighbor 1:1 matching) was applied to conduct a retrospective cohort study in five public tertiary hospitals in the Hubei province of China during 2013-2015. Descriptive analysis, Pearson's chi-squared test, Mann-Whitney U-test, Wilcoxon signed-rank test and paired/independent Z/T test were conducted. The statistically significant level was set at P<0.05.

FINDINGS

From 2013 to 2015 overall, the additional total medical expenditure per HAI-AMR inpatient was US$15,557.25 compared with that of the non-HAIs, and the additional length of per hospital stay of the HAI-AMR inpatient was 41 days compared with that of the non-HAIs (P<0.001).

CONCLUSIONS

In combination with AMR, HAIs caused significant additional medical expenses and affected the turnover rate of hospital beds. Most of the increased medical costs fell to patients and their families. These findings call for more effective control of HAIs and containment of AMR. A national study is needed to estimate the medical, social and economic burden of HAIs in combination with AMR.

Identification of Gram negative non-fermentative bacteria: How hard can it be?

INTRODUCTION

The prevalence of bacteremia caused by Gram negative non-fermentative (GNNF) bacteria has been increasing globally over the past decade. Many studies have investigated their epidemiology but focus on the common GNNF including Pseudomonas aeruginosa and Acinetobacter baumannii. Knowledge of the uncommon GNNF bacteremias is very limited. This study explores invasive bloodstream infection GNNF isolates that were initially unidentified after testing with standard microbiological techniques. All isolations were made during laboratory-based surveillance activities in two rural provinces of Thailand between 2006 and 2014.

METHODS

A subset of GNNF clinical isolates (204/947), not identified by standard manual biochemical methodologies were run on the BD Phoenix automated identification and susceptibility testing system. If an organism was not identified (12/204) DNA was extracted for whole genome sequencing (WGS) on a MiSeq platform and data analysis performed using 3 web-based platforms: Taxonomer, CGE KmerFinder and One Codex.

RESULTS

The BD Phoenix automated identification system recognized 92% (187/204) of the GNNF isolates, and because of their taxonomic complexity and high phenotypic similarity 37% (69/187) were only identified to the genus level. Five isolates grew too slowly for identification. Antimicrobial sensitivity (AST) data was not obtained for 93/187 (50%) identified isolates either because of their slow growth or their taxa were not in the AST database associated with the instrument. WGS identified the 12 remaining unknowns, four to genus level only.

CONCLUSION

The GNNF bacteria are of increasing concern in the clinical setting, and our inability to identify these organisms and determine their AST profiles will impede treatment. Databases for automated identification systems and sequencing annotation need to be improved so that opportunistic organisms are better covered.

Distribution of Toxinogenic Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus from Different Ecological Niches in Algeria

The diffusion of Panton-Valentine leukocidin (PVL)-positive methicillin-resistant S. aureus (MRSA) is a health problem in Algeria. The objectives of the study were to investigate the global distribution of methicillin-susceptible S. aureus (MSSA) and MRSA isolates in different ecological niches in this country. In total, 2246 samples were collected from humans, livestock, wild animals, pets, food products and the aquatic environment, from 12 Algerian provinces. A total of 312 S. aureus were detected from 2446 samples (12.7%) in the screened niches. We observed the emergence of toxinogenic S. aureus representing 41% of the isolates. Among them, we noted the diffusion of ST80-IV CA-MRSA PVL + strains isolated in human, animals, and food and genetic diversity of MSSA PVL + isolates. This study suggests an alarming dissemination of MRSA-ST80 PVL + in both human and extra-human sources in Algeria. Moreover, MSSA may become a permanent reservoir of the PVL genes necessary for human infections.

Point prevalence surveys of health-care-associated infections: a systematic review

Health-care-associated infections (HAIs) are considered a serious public health issues that contribute substantially to the global burden of mortality and morbidity with respect to infectious diseases. The aim is to assess the burden of health-care-associated infections by collation of available data from published point prevalence surveys (PPS) on HAIs to give future guidance. Study protocol and methodology were designed according to preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines. Published research papers that conducted a point prevalence survey of HAIs in hospital settings by following the structured survey methodology employed by European Centre of Disease Prevention and Control (ECDC) were included. Of 1212 articles, 67 studies were included in the final analysis conducted across different countries. Overall, 35 studies were conducted in Europe, 21 in Asia, 9 in America, and 2 in Africa. The highest prevalence of HAIs was recorded in a study conducted in adult ICU settings of 75 regions of Europe (51.3%). The majority of the studies included HAI data on urinary tract infections, respiratory tract infections, and bloodstream infections. Klebsiella pneumonia, Pseudomonas aeruginosa and E. coli were the most frequent pathogens responsible for HAIs. PPS is an useful tool to quantify HAIs and provides a robust baseline data for policymakers. However, a standardize surveillance method is required. In order to minimize the burden of HAIs, infection prevention and control programs and antibiotic stewardship may be effective strategies to minimize the risk of HAIs.