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International Journal of Molecular... Apr 2024Molecular methods have become integral to microbiological research for microbial identification. This literature review focuses on the application of molecular methods... (Review)
Review
Molecular methods have become integral to microbiological research for microbial identification. This literature review focuses on the application of molecular methods in examining airborne bacteria and fungi in healthcare facilities. In January 2024, a comprehensive electronic search was carried out in esteemed databases including PubMed, Web of Science, and Scopus, employing carefully selected keywords such as ((bacteria) OR (virus) OR (fungi)) AND (aerosol) AND ((hospital) OR (healthcare) OR (dental office)) AND ((molecular) OR (PCR) OR (NGS) OR (RNA) OR (DNA) OR (metagenomic) OR (microarray)), following the PRISMA protocol. The review specifically targets healthcare environments with elevated concentrations of pathogenic bacteria. A total of 487 articles were initially identified, but only 13 met the inclusion criteria and were included in the review. The study disclosed that the prevalent molecular methodology for appraising aerosol quality encompassed the utilization of the PCR method, incorporating either 16S rRNA (bacteria) or 18S rRNA (fungi) amplification techniques. Notably, five diverse molecular techniques, specifically PFGE, DGGE, SBT, LAMP, and DNA hybridization methods, were implemented in five distinct studies. These molecular tests exhibited superior capabilities compared to traditional bacterial and fungal cultures, providing precise strain identification. Additionally, the molecular methods allowed the detection of gene sequences associated with antibiotic resistance. In conclusion, molecular testing offers significant advantages over classical microbiological culture, providing more comprehensive information.
Topics: Fungi; Aerosols; Bacteria; Air Microbiology; Humans; Health Facilities
PubMed: 38673740
DOI: 10.3390/ijms25084154 -
Antibiotics (Basel, Switzerland) Mar 2024Antimicrobial resistance (AMR) is a growing public health problem in the One Health dimension. Artificial intelligence (AI) is emerging in healthcare, since it is... (Review)
Review
Antimicrobial resistance (AMR) is a growing public health problem in the One Health dimension. Artificial intelligence (AI) is emerging in healthcare, since it is helpful to deal with large amounts of data and as a prediction tool. This systematic review explores the use of AI in antimicrobial stewardship programs (ASPs) and summarizes the predictive performance of machine learning (ML) algorithms, compared with clinical decisions, in inpatients and outpatients who need antimicrobial prescriptions. This review includes eighteen observational studies from PubMed, Scopus, and Web of Science. The exclusion criteria comprised studies conducted only in vitro, not addressing infectious diseases, or not referencing the use of AI models as predictors. Data such as study type, year of publication, number of patients, study objective, ML algorithms used, features, and predictors were extracted from the included publications. All studies concluded that ML algorithms were useful to assist antimicrobial stewardship teams in multiple tasks such as identifying inappropriate prescribing practices, choosing the appropriate antibiotic therapy, or predicting AMR. The most extracted performance metric was AUC, which ranged from 0.64 to 0.992. Despite the risks and ethical concerns that AI raises, it can play a positive and promising role in ASP.
PubMed: 38666983
DOI: 10.3390/antibiotics13040307 -
Brazilian Journal of Microbiology :... Jun 2024In South Africa, basic healthcare centres treat sexually transmitted infections (STIs) using a syndromic approach. In line with Preferred Reporting Items for Systematic... (Review)
Review
In South Africa, basic healthcare centres treat sexually transmitted infections (STIs) using a syndromic approach. In line with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) recommendations, a complete study of all randomised controlled trials and surveillance data relevant to N. gonorrhoeae antibiotic resistance was conducted. To discover papers published between 2002 and 2022, searches were undertaken using PubMed, EMBASE and any other relevant databases. This systematic review extracted a total of 463 articles published between 2002 and 2022 from a variety of online research sources. Seven South African provinces were represented in the studies that were assessed. Mpumalanga and the North West Province did not have any studies that described the identification and monitoring of antimicrobial resistance (AMR). This study presents data obtained from a comprehensive analysis of 2140 isolates, in which we examined the presence of one or more antibiotic resistance. Our findings revealed that out of these samples, 1891 isolates exhibited antimicrobial properties; tetracycline was the antimicrobial resistance that was found the most often (30%), followed by ciprofloxacin (19%) and penicillin (17%). The mean of the isolates was 143, the upper 95% mean was 243, and the standard deviation (SD) was 181.6. All microbiological identification and susceptibility testing processes must be standardised and improved so national organisations can monitor AMR. The nation's health community must address all identified areas of concern to avoid AMR.
Topics: South Africa; Neisseria gonorrhoeae; Gonorrhea; Humans; Anti-Bacterial Agents; Drug Resistance, Bacterial; Microbial Sensitivity Tests
PubMed: 38662152
DOI: 10.1007/s42770-024-01281-6 -
Journal of Infection and Public Health Jun 2024Wild birds could be a reservoir of medically relevant microorganisms, particularly multidrug-resistant Enterococcus spp. Resistant bacteria's epidemiology and... (Meta-Analysis)
Meta-Analysis
Wild birds could be a reservoir of medically relevant microorganisms, particularly multidrug-resistant Enterococcus spp. Resistant bacteria's epidemiology and transmission between animals and humans has grown, and their zoonotic potential cannot be ignored. This is the first study to evaluate the status of vancomycin resistant enterococci (VRE) in various wild bird species using meta-analysis and a systematic review. In this study, the pooled prevalence was obtained by analyzing data from published articles on the occurrence of VRE in wild bird species. It's unclear how the antibiotic resistance gene transfer cycle affects wild birds. Google Scholar and PubMed were used to conduct the research. The data and study methodology was assessed and extracted by two reviewers independently, with a third reviewing the results. Heterogeneity between study and publication bias were analyzed using the random effect model. Thirty-eight studies were included in the meta-analysis. 382 out of the 4144 isolates tested, were VRE. The pooled prevalence of VRE among wild birds was estimated at 11.0% (95% CI; 6.9 -17.2%; I = 93.204%; P < 0.001). There was high variability between study (t = 2.156; heterogeneity I = 93.204% with chi-square (Q) = 544.413, degrees of freedom (df) = 37, and P < 0.001). Egger's test verified the funnel plot's bias, while result from the leave-one-out forest plot had no effect on the pooled prevalence.
Topics: Animals; Animals, Wild; Birds; Gram-Positive Bacterial Infections; Prevalence; Vancomycin-Resistant Enterococci
PubMed: 38657438
DOI: 10.1016/j.jiph.2024.04.004 -
Cureus Mar 2024Antibiotic resistance is a global public health concern that poses a significant threat to the effective treatment of bacterial infections. , a family of gram-negative... (Review)
Review
Antibiotic resistance is a global public health concern that poses a significant threat to the effective treatment of bacterial infections. , a family of gram-negative bacteria, are associated with a wide range of infections, including urinary tract infections, bloodstream infections, and respiratory tract infections. This systematic review aimed to examine the antibiotic resistance trend among in Saudi Arabia in the period between 2003 and 2023. Five databases (PubMed, Medline, Ovid, Scopus, and Cochrane) were searched using the keywords "Resistance AND Enterobacteriaceae AND Saudi Arabia" in the title and abstract. All papers assessing the prevalence of resistance among in Saudi Arabia were included in the systematic review. Out of 97 papers that were extracted through the database search, 22 articles were considered suitable for the systematic review. The articles included 17027 isolates, out of which 7592 isolates were identified as resistant bacteria. The studies included various resistant strains, such as and , that were responsible for various clinical conditions, including urinary tract infections, blood infections, surgical site infections, and pneumonia. In addition, the review highlighted the dynamic nature of antibiotic resistance, with the identification of new resistant bacterial species and the emergence of resistance to newer antibiotic classes over the last decade. Continued surveillance, rational antibiotic use, and the development of alternative treatment options are crucial to address the evolving landscape of antibiotic resistance among bacteria in the country.
PubMed: 38646237
DOI: 10.7759/cureus.56614 -
Annals of Intensive Care Apr 2024Drowning-associated pneumonia (DAP) is frequent in drowned patients, and possibly increases mortality. A better understanding of the microorganisms causing DAP could... (Review)
Review
BACKGROUND
Drowning-associated pneumonia (DAP) is frequent in drowned patients, and possibly increases mortality. A better understanding of the microorganisms causing DAP could improve the adequacy of empirical antimicrobial therapy. We aimed to describe the pooled prevalence of DAP, the microorganisms involved, and the impact of DAP on drowned patients.
METHODS
Systematic review and meta-analysis of studies published between 01/2000 and 07/2023 reporting on DAP occurrence and microorganisms involved.
RESULTS
Of 309 unique articles screened, 6 were included, involving 688 patients. All were retrospective cohort studies, with a number of patients ranging from 37 to 270. Studies were conducted in Europe (France N = 3 and Netherland N = 1), United States of America (N = 1) and French West Indies (N = 1). Mortality ranged between 18 to 81%. The pooled prevalence of DAP was 39% (95%CI 29-48), similarly following freshwater (pooled prevalence 44%, 95%CI 36-52) or seawater drowning (pooled prevalence 42%, 95%CI 32-53). DAP did not significantly impact mortality (pooled odds ratio 1.43, 95%CI 0.56-3.67) but this estimation was based on two studies only. Respiratory samplings isolated 171 microorganisms, mostly Gram negative (98/171, 57%) and mainly Aeromonas sp. (20/171, 12%). Gram positive microorganisms represented 38/171 (22%) isolates, mainly Staphylococcus aureus (21/171, 12%). Water salinity levels had a limited impact on the distribution of microorganisms, except for Aeromonas sp. who were exclusively found following freshwater drowning (19/106, 18%) and never following seawater drowning (0%) (p = 0.001). No studies reported multidrug-resistant organisms but nearly 30% of the isolated microorganisms were resistant to amoxicillin-clavulanate, the drug that was the most commonly prescribed empirically for DAP.
CONCLUSIONS
DAP are commonly caused by Gram-negative bacteria, especially Aeromonas sp. which is exclusively isolated following freshwater drowning. Empirical antimicrobial therapy should consider covering them, noting than amoxicillin-clavulanate may be inadequate in about one-third of the cases. The impact of DAP on patients' outcome is still unclear.
PubMed: 38641650
DOI: 10.1186/s13613-024-01287-1 -
Open Veterinary Journal Jan 2024Antimicrobial resistance (AMR) is recognized globally as a significant health challenge, but its extent remains unclear in many regions. It is crucial to prioritize a...
BACKGROUND
Antimicrobial resistance (AMR) is recognized globally as a significant health challenge, but its extent remains unclear in many regions. It is crucial to prioritize a foundational evaluation of AMR prevalence to facilitate the implementation of laboratory-based surveillance. Adopting a One Health perspective, this study outlines the present AMR status in the Middle East.
AIM
To synthesize the current state of knowledge on AMR in the Middle East, delineate the contributions of different sectors (human health, animal health, and environment), and discern the effectiveness of One Health interventions in mitigating AMR.
METHODS
An exhaustive literature search was conducted via PubMed, ScienceDirect, and Google Scholar. Potential articles were screened and assessed for eligibility based on prescribed eligibility criteria. Data synthesis was done, and the results were reported and discussed thematically.
RESULTS
Twenty-three studies were included in the study and published between 2019 and 2023. Most studies reveal substantial challenges in treating infections, with a significant prevalence of resistance in critical care units, particularly against extended-spectrum beta-lactamases and carbapenem-resistant Gram-negative bacteria. Colistin and imipenem resistance in pediatric populations further emphasize the urgency of understanding and addressing diverse resistance mechanisms in the region. Studies on urinary pathogens, bacteremia, and biofilm formation highlight the multifaceted challenge of AMR. The emergence of resistance to key antibiotics emphasizes the urgency for tailored treatment strategies.
CONCLUSION
Given the interconnectedness of human, animal, and environmental health, a One Health perspective is imperative. The diverse challenge demands coordinated efforts, including innovative interventions and public health policies. Bridging existing gaps through future research is crucial for evidence-based and context-specific strategies in combating AMR in the region.
Topics: Humans; Animals; Anti-Bacterial Agents; Drug Resistance, Bacterial; One Health; Carbapenems; Bacteria; Middle East
PubMed: 38633186
DOI: 10.5455/OVJ.2024.v14.i1.53 -
Journal of Epidemiology and Global... Jun 2024Due to the rising incidence of multidrug-resistant (MDR) pathogens, especially in Low-Middle-Income Countries (LMIC), post-partum infections represent a significant... (Review)
Review
BACKGROUND
Due to the rising incidence of multidrug-resistant (MDR) pathogens, especially in Low-Middle-Income Countries (LMIC), post-partum infections represent a significant treatment challenge.
METHODS
We performed a systematic review of the literature from January 2005 to February 2023 to quantify the frequency of maternal post-partum infections due to MDR pathogens in LMICs, focusing on methicillin-resistant Staphylococcus aureus (MRSA) and/or extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales.
SECONDARY OBJECTIVES
description of antimicrobials' prescriptions.
FINDINGS
We included 22 studies with 14,804 total bacterial isolates from 12 countries, mostly from WHO African-Region. Twelve papers described wound- and 10 puerperal-infections. Seven were high-quality articles. Seventeen studies reported data on MRSA, and 18 on ESBL-producing Enterobacterales. Among high-quality studies, MRSA ranged from 9.8% in Ghana to 91.2% in Uganda; ESBL-producing Enterobacterales ranged from 22.8% in Ukraine to 95.2% in Uganda. Nine articles, mostly on C-sections, described different protocols for antibiotic prophylaxis and/or post-partum treatment.
INTERPRETATION
We described a high burden of post-partum infections caused by MRSA and/or ESBL-producing Enterobacterales in LMICs, but only a few studies met quality standards. There is an urgent need for high-quality studies to better describe the real burden of antimicrobial resistance in low-resource settings and inform policies to contain the spread of multidrug-resistant organisms.
Topics: Humans; Female; Developing Countries; Puerperal Infection; Methicillin-Resistant Staphylococcus aureus; Anti-Bacterial Agents; Pregnancy; Drug Resistance, Multiple, Bacterial; Staphylococcal Infections; Postpartum Period
PubMed: 38630391
DOI: 10.1007/s44197-024-00222-8 -
Frontiers in Public Health 2024The spread of antimicrobial resistance (AMR) is a major global concern, and the islands of the Southwest Indian Ocean (SWIO) are not exempt from this phenomenon. As... (Review)
Review
The spread of antimicrobial resistance (AMR) is a major global concern, and the islands of the Southwest Indian Ocean (SWIO) are not exempt from this phenomenon. As strategic crossroads between Southern Africa and the Indian subcontinent, these islands are constantly threatened by the importation of multidrug-resistant bacteria from these regions. In this systematic review, our aim was to assess the epidemiological situation of AMR in humans in the SWIO islands, focusing on bacterial species listed as priority by the World Health Organization. Specifically, we examined Enterobacterales, spp., spp. resistant to carbapenems, and spp. resistant to vancomycin. Our main objectives were to map the distribution of these resistant bacteria in the SWIO islands and identify the genes involved in their resistance mechanisms. We conducted literature review focusing on Comoros, Madagascar, Maldives, Mauritius, Mayotte, Reunion Island, Seychelles, Sri Lanka, and Zanzibar. Our findings revealed a growing interest in the investigation of these pathogens and provided evidence of their active circulation in many of the territories investigated. However, we also identified disparities in terms of data availability between the targeted bacteria and among the different territories, emphasizing the need to strengthen collaborative efforts to establish an efficient regional surveillance network.
Topics: Humans; Anti-Bacterial Agents; Drug Resistance, Bacterial; Indian Ocean Islands
PubMed: 38628847
DOI: 10.3389/fpubh.2024.1357345 -
PloS One 2024Pretreatment drug resistance (PDR) could occur in antiretroviral treatment (ART) naïve individuals, those previously exposed to ART, or individuals re-initiating ARV... (Meta-Analysis)
Meta-Analysis
INTRODUCTION
Pretreatment drug resistance (PDR) could occur in antiretroviral treatment (ART) naïve individuals, those previously exposed to ART, or individuals re-initiating ARV after a long period of interruption. Few studies have shown its association with virological outcomes, although inconsistent. The objective of this review was to provide a synthesis of the association between PDR and virological outcomes (virological failure or suppression).
METHODS
This report is presented following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The method was subdivided into three main phases: record identification, screening, and report inclusion. Record identification consisted of an initial search with search term "HIV pretreatment drug resistance". Another search was done using terms "Pretreatment drug resistance OR pre-treatment drug resistance OR Pretreatment drug resist* OR pre-treatment drug resist* OR pretreatment antiretroviral resistance OR pretreatment medic* OR pretreatment medic* resist*" and a list of all the countries in sub-Saharan Africa. After the electronic search, studies were screened from full list based on their title and abstract and then full articles retrieved and studies were assessed based on set criteria. Inclusion criteria involved observational studies that report the association between PDR and virological failure. Data from trials that reported the association were also included. Published articles like modelling studies and reviews, and studies with data that had been previously included in the review were excluded. The Mantel Haenszel method with odds ratios was used for synthesis (meta-analyses) with the weights of each study which depends on the number of events and totals.
RESULTS
A total of 733 records(studies) were obtained from all database search of which 74 reported on PDR, virological outcomes in sub-Saharan Africa (SSA). Out of the 74 articles, 11 were excluded and 26 did not explicitly report data needed, and 5 did not meet the inclusion criteria. Of the remaining 32 studies, 19 studies that had complete data on the number of participants with PDR and no PDR according to virological failure (VF) were included in the metanalyses. The pooled results from eleven (13) of these studies showed those with PDR had higher odds of virological failure compared to those without PDR OR 3.64[95% CI 2.93, 4.52]. The result was similar when stratified in adults and in children. In six (6) studies that had Virological suppression (VS) as outcome, there was a reduction in the odds of VS in those with PDR compared to those without PDR, OR 0.42 (95% CI 0.30, 0.58).
CONCLUSION
In conclusion, this systematic review indicates that PDR increases the risk of virological failure in sub-Saharan Africa. The risk could be reduced by PDR monitoring for NNRTIs and INSTIs.
Topics: Adult; Child; Humans; Anti-HIV Agents; HIV Infections; HIV-1; Anti-Retroviral Agents; Africa South of the Sahara; Drug Resistance, Viral; Viral Load
PubMed: 38626183
DOI: 10.1371/journal.pone.0300456