FormalPara Key Summary Points

Healthcare-associated infections (HAIs) development could be seriously influenced by factors like prolonged hospital stays, medical devices, and specific comorbidities.

The combination of molecular diagnostic techniques, microbiome-based solutions, and artificial intelligence-powered systems has significantly improved HAIs management.

Phage therapy is an emerging option that can provide an alternative to ineffective antibiotic treatments for HAIs causative bacteria.

Clinical trials dealing with vaccine development for multidrug-resistant bacteria have yielded conflicting results.

In the era of the climate crisis, life-threatening infectious diseases could still be reduced by implementing One Health strategies.

Introduction

Healthcare-associated infections (HAIs), previously known as nosocomial infections, represent a significant challenge for healthcare systems worldwide [1, 2].

These infections are among the most significant complications associated with modern medical therapy, being directly influenced by the high use of invasive medical devices, inappropriate use of antimicrobial therapy, patient age, and immunological status [3,4,5,6]. Globally, HAIs are a significant public health problem, contributing to the prolongation of patient hospital stays and antimicrobial therapy. Thus, HAIs have a significant impact on the selection of resistant bacteria, generating high costs for health systems [6,7,8,9,10,11,12]. Recent reports have shown that for every 100 hospitalized patients, seven patients in high-income countries and 10 in low- and middle-income countries contract at least one type of HAI, and of these patients, 10% die.

The most prevailing types of HAIs exhibiting increased risk of complications are non-ventilator-associated hospital-acquired pneumonia [13], urinary tract infections [14], and sepsis [15]. These representative HAIs responsible for worldwide death are caused by multidrug-resistant (MDR) bacteria, including MDR Gram-negative bacilli, vancomycin-resistant enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA), and Clostridioides difficile [6, 11, 16,17,18,19,20]. The global burden produced by HAIs at the individual, community and public levels could be decreased by implementing appropriate infection prevention and control (IPC) policies and strategies [9, 21]. However, in the absence of IPC infrastructure, and due to inappropriate antibiotic use in clinical settings and industrial facilities contributing to environmental contamination, HAIs outbreaks could spread very quickly in healthcare facilities and outside [22].

Human activities such as massive land changes, pollution, and biodiversity loss [23, 24] lead to critical environmental distortions, which could increase the HAI expansion through antibiotic and pesticide emissions [11, 25]. Recent data endorse the close connection between the climate crisis and the rise of heavy metals or biocides concentrations in soil and water, influencing antimicrobial resistance (AMR) by co-/cross-resistance mechanisms [26,27,28,29,30,31]. Consequently, there is a pressing need to understand the effects of environmental change on the rise of HAIs and to propose solutions to mitigate this severe public health crisis [22, 32].

This review presents the prevalence, risk factors, current diagnosis, including artificial intelligence and machine learning approaches, future perspectives in combating HAIs causative bacteria (phage therapy, microbiome-based interventions, and vaccination), and strategies for preventing and controlling HAIs. Also, we discuss the latest findings regarding the relationships of antibiotic resistance (AR) with climate change and environmental pollution in the context of the One Health approach. Although numerous papers explore these aspects, our paper provides an integrated perspective by incorporating the latest research, particularly regarding advanced omics approaches in HAI diagnostic and emerging therapeutic strategies. These aspects are essential for providing pathogens comprehensive identification and mitigating life-threatening illnesses caused by HAIs causative bacteria. Unlike prior studies, which often discuss the results from preclinical studies, this review incorporates the recent clinical trials focused on exploring novel therapeutic strategies and addressing current challenges. This article is based on previously conducted studies and does not contain any new studies with human participants or animals performed by any of the authors.

Search Methodology and Inclusion Criteria

A structured approach was applied to ensure coverage of key studies rather than exhaustive systematic screening. For this purpose, relevant publications were searched from 2005 to 2025 using the databases ScienceDirect, PubMed, Springer Nature, and Google Scholar. The search strategy involved the use of keywords and medical subject heading (MeSH) terms, such as “healthcare-associated infections,” “antimicrobial therapy,” “phage therapy,” “vaccines,” “dysbiosis,” One-Health, “climate change,” and “microbiome.” Various Boolean operators (“OR” and “AND”) were employed to develop the search strategies. The search was conducted from 15 October to 10 March 2025, and all English-published articles available online until the day of data collection were considered. The search terms were refined based on preliminary searches, and duplicate studies were removed.

Prevalence of HAIs at the International Level

An observational study by the World Health Organization (WHO) [33] between 1995 and 2010 reported a 7.6% prevalence in developed countries. In Europe, it is estimated that annually, over 4 million patients are affected by HAIs. The same study reported a 4.5% incidence in the USA, while in low-income countries, the incidence is much higher (up to 88.9%) [33]. In 2016, WHO reported a prevalence rate of HAIs in low- and middle-income countries (LMIC) of 5.7–19.1%. A more recent study reports a HAIs prevalence variation from 7% in developed countries to 30% in LMIC, a difference that could be explained, at least partially, by the insufficient training of healthcare personnel, limited resources, and non-compliance with infection control measures [34]. However, these data could be biased by inadequate data storage infrastructure and resources [9, 11, 35, 36].

The HAIs prevalence is higher in intensive care units (ICUs). In a multicenter study conducted by WHO in 2010, the prevalence of HAIs in ICUs was 51%, which led to prolonged hospitalization and an increased risk of other infections and complications [37]. Hazard and collaborators reported a rate of 17 cases of HAIs per 1000 days of hospitalization in ICUs in developed countries [38].

In neonates, the prevalence of HAIs caused by extended-spectrum beta-lactamase (ESBL)-producing bacteria has been reported to be as high as 11% (cumulative prevalence was 15% in Africa, 12% in South America, 11% in India, 7% in the rest of Asia, 4% in Europe and 0% in Oceania) and is increasing by approximately 3.2% per year. HAIs caused by ESBLs is associated with a mortality rate twice as high as HAIs caused by other organisms, 36% versus 18% [39].

In the European Area, over 2.5 million new cases of HAIs are reported annually [7, 9, 11]. According to the last report of the European Centre for Disease Prevention and Control (ECDC) [40], approximately 4.3 million patients acquired at least one HAI per year in European acute care hospitals in 2022–2023. The most common HAIs cases reported were respiratory tract infections, urinary tract infections, surgical wound infections, sepsis, and gastrointestinal infections. The report provides data supporting the expansion of resistance due to the abusive use of antibiotics, which has led to limited treatment options. It is estimated that at least 20% of HAIs could be prevented by sustained and comprehensive IPC programs, including simple measures such as appropriate hand hygiene [40].

In Italy, the HAIs overall prevalence has been 8.4%, with a higher frequency in patients admitted to smaller hospitals, in ICUs, and among patients using invasive medical devices, the HAIs being associated with a significant expansion of AR [6]. While a study reported an overall prevalence of HAIs of 7.6% [41] in Italy, a significant decrease from 5% in 2009 to 2.1% in 2019 has been reported [42].

Annually, HAIs are diagnosed in approximately 1.7 million people in the United States, with a prevalence of 4.5% and 90,000–99,000 people dead [7].

Goh and collaborators led a systematic review based on 31 studies, including 47,666 participants and 7658 HAIs cases from Southeast Asia, disclosing a 21.6% prevalence of these infections with significant disparities across regions. The results unveiled that the highest prevalence was registered in Indonesia (30.4%) and the lowest in Singapore (8.4%) [43].

In South Korea, despite infection control measures [44,45,46], the COVID-19 pandemic influenced significantly the HAIs management, particularly in the immunosuppressed patients [47,48,49,50,51]. This fact is sustained by the results of Oh and collaborators, who found that the incidence of common respiratory virus (cRV) infections diminished significantly after implementing IPC measures for COVID-19. However, they observed increased C. difficile infections and the incidence rates of VRE and carbapenemase-producing Enterobacterales (CPE) strains in immunosuppressed patients [52].

A systematic review of 19 studies in Africa indicated a prevalence of HAIs between 2.5% and 14.8%, with surgical wound infections and the involvement of Gram-negative bacteria frequently reported [6, 53]. Other studies reported that E. coli (18.3%), S. aureus (17.3%), Klebsiella spp. (17.2%), Pseudomonas spp. (10.3%) and Acinetobacter spp. (6.8%) strains were the most common [54], indicating a prevalence of HAI of up to 50% in ICUs. However, due to the significant percentage obtained within specific institutions, these reports may not reflect the situation at the national level [6, 53,54,55].

In Tanzania, a cross-sectional study of 134 patients from different clinical departments revealed a prevalence of 15.7% of HAI, an unusually high value for a tertiary care clinical unit [34].

In Australia, data analysis from 2017–2019 indicates that 75–80% of HAIs are reported in New South Wales, Victoria, and Queensland, with S. aureus bacteremia being the only indicator consistently tracked nationally. With an estimated prevalence of 9.9% according to a 2018 study and approximately 83,096 cases reported annually, this data allows hospitals to evaluate the effectiveness of interventions to reduce HAsI and increase transparency regarding infection rates [56].

In New Zealand, an observational study including 5468 patients indicated a prevalence of HAIs of 6.6% among hospitalized patients. The most common types of HAIs were surgical site infections (25%), urinary tract infections (18%), and sepsis (13%). Approximately 66% of patients had at least one medical device, such as a peripheral intravenous catheter, leading to 16% of HAIs associated with medical devices [57].

In Thailand, research by Moolasart and collaborators revealed a 3.9% prevalence of HAIs in pediatric inpatients and found that more extended hospitalization periods and central venous catheters (CVCs) were the most important risk factors [58].

In Papua New Guinea, based on ECDC protocol, Curtis and collaborators did a point prevalence survey on HAIs and registered a 6.7% prevalence in a national hospital. However, when the authors estimated prevalence through an extended HAI definition that combined infections identified by the ECDC criteria with a physician diagnosis, the HAIs overall prevalence increased to 12.4% This study provides essential baseline data for prioritizing interventions and monitoring future changes [59].

One of the most serious consequences of HAIs is the increase in the rate of AR generated by the frequent and sometimes incorrect use of antibiotics, which leads to the natural selection of resistant bacteria, making treatment difficult and expensive, with direct consequences for the safety of patients and healthcare personnel. Almost all pathogenic microorganisms have developed resistance to antimicrobial agents [12]. A study conducted in the USA by Teillant et al. estimated that by 2050, the increase in AR could cause a global economic loss of approximately $300 trillion in global gross domestic product [60, 61].

HAIs caused by MDR bacteria are associated with prolonged hospital stay and antibiotic use, additional treatment costs, and increased readmission rates, favoring higher risk of morbidity and mortality [20, 26, 38, 54, 62,63,64,65]. In the United States, these costs range from $28.4 billion to $45 billion, thus exerting significant financial pressure on the public health system, considering that such events can be prevented by alignment to workplace conduct, procedures, and IPC guidelines [12, 38, 54, 66,67,68,69]. In Africa, MDR bacteria were common: 70.3% of Enterobacterales strains were resistant to 3rd generation cephalosporins. In comparison, 70.5% of S. aureus strains were methicillin-resistant, and 55% of P. aeruginosa strains were resistant to all agents tested [54].

The studies presented before demonstrate that several factors like healthcare infrastructure, socioeconomic factors, IPC practices influence the prevalence of HAIs across different regions, explaining the lower prevalence rates (4.5–9.9%) in high-income countries compared to LIMCs (5.7–21.6%). In resource-limited settings, HAIs are exacerbated by infrastructure issues, such as the lack of safe water in hospitals, inadequate sanitation and sanitation systems, understaffing, lack or failure to enforce health policies on antibiotic use, lack of essential laboratory equipment for diagnosis, failure to follow safety practices by health professionals, low reporting rates, and limited financial resources [54, 70, 71].

HAIs are still a significant global challenge, with various prevalence rates depending on IPC policies, healthcare infrastructure, and socioeconomic factors. High-income countries report lower prevalence (4.5–9.9%), while low- and middle-income countries (LMICs) experience significantly higher rates (5.7–21.6%), resistance percentages varying due to incorrect use of antibiotics, inadequate sanitation, and limited resources. ICUs are particularly affected, and HAI rates lead to increased morbidity, mortality, and financial burdens—ranging from $28.4 billion to $45 billion annually in the U.S. alone. Despite the improvements made by several developed in the long-term reduction of HAI incidence, there are still shortcomings in regions facing infrastructural and financial constraints [54]. Therefore, a coordinated strategy bringing together technological advancements with context-specific interventions is critically needed to bridge these gaps and develop appropriate IPC practices [38, 64].

Risk Factors Associated with HAIs

Specific comorbidities, such as diabetes mellitus [72], advanced patient age [73], dementia, use of antipsychotics, stroke, length of hospital stay, type of care (especially rehabilitation and short-term care, use of medical devices (urethral catheters, suprapubic catheters, tracheostomies, peripheral venous catheter, peripheral central access catheter, CVC, urinary catheters, nasogastric tubes) and duration of the placement may be important risk factors for nosocomial infections [20, 42, 74,75,76,77,78] (Fig. 1).

Fig. 1
Fig. 1
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Schematic representation of the risk factors linked with HAIs (created with Adobe Illustrator CS6, Adobe Photoshop CS3)

Diabetes mellitus, in particular, significantly increases the risk of urinary tract infections, while its role as a risk factor for healthcare-associated pneumonia remains a matter of debate [20, 72, 79, 80].

The prevalence of nosocomial infections among elderly patients is higher and the presence of neurological diseases in the elderly is an additional risk factor for contracting HAIs [20, 81, 82]. Related to this, although there is little evidence to support this, some studies suggest that antipsychotic medications, commonly used in neurology, could be an underestimated risk factor for nosocomial infections, especially pneumonia [83]. Taking into account that HAIs and the length of hospital stay are synergistically interconnected, the average length of hospital stay is significantly longer in geriatric patients with neurological diseases compared to the average length of hospital stay of other patient categories [20]. In newborns, HAIs are common and can be extremely dangerous, especially those caused by ESBL bacteria [84]. According to the ECDC, the prevalence of HAIs in children is almost 4%. However, this percentage is more than double in neonatal intensive care units (NICUs), where more than one in ten newborns develop some type of HAI [85]. Unfortunately, current prevention measures could not entirely address these high-risk groups in specific clinical settings like NICUs and geriatric care.

To conclude, various comorbidities (diabetes mellitus, dementia, and stroke), together with the use of medical devices (e.g., catheters, tracheostomies, and central venous catheters), significantly elevate the risk of HAIs. For patients with diabetes mellitus and urinary tract infections, its role in healthcare-associated pneumonia remains debated. In children, the prevalence of HAIs caused by ESBL-producing bacteria is around 4% but could affect over 10% of newborns. High-risk groups such as geriatric and neonatal patients remain particularly vulnerable, requiring the need for targeted IPC strategies and improved monitoring.

Advanced Diagnostic Approaches for HAIs

A timely and accurate diagnosis of HAIs is essential for the implementation of effective IPC measures and appropriate antimicrobial therapy, to reduce the burden of HAIs in terms of morbidity, mortality, and healthcare costs.

Despite their widespread use in routine diagnostic laboratories, traditional microbiological methods, such as culture-based techniques, present significant limitations, due to prolonged response time, sensitivity as well as the complexity and costs the required procedures [86].

Recent advancements in molecular diagnostics such as polymerase chain reaction (PCR)-based qualitative or quantitative assays, matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS), and next-generation sequencing (NGS) empowered by artificial intelligence (AI) and machine learning (ML) systems have revolutionized the rapid, accurate, and comprehensive identification of pathogens involved in HAIs [87, 88] (Fig. 2).

Fig. 2
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Workflow for complete and accurate diagnosis of HAIs. (1) Sample collection in HAI diagnosis (surgical wounds, blood, urine, and bronchial aspirates); (2) Isolation of the pure culture and identification by conventional methods (antibiotic susceptibility testing and biochemical identification); (3) DNA isolation and identification by NGS (bacterial DNA and 16S rRNA isolation and sequencing); (4) MS workflow for identifying microorganisms involves placing a fresh colony or biological samples on a MALDI target microplate, which will then be analyzed by mass spectrometry (created with Adobe Illustrator CS6, Adobe Photoshop CS3)

PCR technologies

PCR is used to detect MDR bacterial pathogens involved in the etiology of HAIs, especially those from the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) and Clostridioides difficile [86, 89]. However, the epidemiological variations that appeared in the last years unveiled the need to change the initial proposed acronym “ESKAPE” to “ESCAPE” (E. faecium, S. aureus, Clostridioides difficile, A. baumannii, P. aeruginosa, and Enterobacteriaceae) [90].

PCR is also highly effective in detecting nosocomial viral infections, such as cytomegalovirus (CMV), norovirus, and respiratory viruses [91], but also in the rapid detection of Candida sp. and Aspergillus sp. infections. At the same time, multiplex PCR panels for the rapid detection of sepsis within hours, thus improving the early antimicrobial therapy, are available [92].

Based on PCR technology, real-time PCR (RT-PCR) is one of the most clinically used techniques for diagnosing infectious diseases. This technique allows real-time monitoring of the target amplification using either unspecifically intercalating fluorescent dyes or specific fluorescently labeled probes [93]. Various PCR platforms have focused on the most prevalent carbapenemases, such as blaKPC, blaOXA-48, blaOXA-23, blaOXA24/40, blaNDM, blaVIM, and blaIMP [94, 95]. Accordingly, a study by Cerezales and collaborators developed a multiplex PCR to identify the most prevalent carbapenemase-encoding genes in 546 carbapenem-resistant isolates retrieved in Germany. They designed primers for 14 carbapenemases, including bla VIM, bla OXA-48, bla OXA-23, blaKPC, blaNDM, blaOXA-40, blaOXA-58, blaIMP, blaGIM, blaGES, ISAba1-blaOXA-51, blaIMI, blaFIM, and blaDIM, allowing real-time monitoring of the target amplification [95].

Advances in RT-PCR have led to various isothermal amplification techniques, including loop-mediated amplification (LAMP), helicase-dependent amplification (HDA), nucleic acid sequence-based amplification (NASBA), and transcription-mediated amplification (TMA).

Unlike conventional PCR, LAMP uses a DNA polymerase with high strand displacement activity and four primers able to distinguish six–to eight distinct regions of the target DNA [96]. Certain commercial LAMP kits have been developed for the detection of resistance genes, such as blaKPC and blaNDM-1, in K. pneumoniae, A. baumannii, Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, and S. aureus [97,98,99,100,101].

NASBA and TMA isothermal amplification reactions are based on various mRNAs as target sequences [102]. In contrast, HDA uses the unwinding activity of a helicase to separate dsDNA into two single strands that can serve as a template for new DNA synthesis [103]. HDA, NASBA, and TMA techniques have been successfully applied to detect Clostridium difficile, S. aureus, E. coli, Chlamydia trachomatis, and N. gonorrhea [103, 104].

Several PCR-based assays have been developed to identify prevalent carbapenemase-encoding genes (e.g., blaKPC, blaOXA-48, blaNDM, blaVIM, blaIMP). At the same time, advances in isothermal amplification techniques, such as LAMP, HDA, NASBA, and TMA, and development of commercial kits have improved diagnostic efficiency by enabling rapid and sensitive detection of broad bacterial strains (e.g., K. pneumoniae, A. baumannii, E. coli, P. aeruginosa, Salmonella enterica, S. aureus, C. difficile, Chlamydia trachomatis, and N. gonorrhea).

MALDI-TOF

MALDI-TOF MS is a mass spectrometry-based technique that identifies microorganisms based on their protein profiles. The mass spectra of bacterial or fungal isolates are compared to a reference database for species-level identification (Fig. 2) [105, 106].

Since its recent introduction into clinical and microbiological diagnostics, MALDI-TOF MS technology has undergone considerable expansion, emerging as a remarkably accurate tool for microorganism identification [107, 108]. In comparison to traditional methods, it is quick, effective, simple to use, and inexpensive, shortening the time until beginning treatment for a sick patient [107, 109,110,111,112]. Both bacterial and fungal pathogens can be successfully identified by MALDI-TOF MS [113].

Rensner and collaborators integrated a deuterium-based labeling method with Bruker MALDI-TOF Biotyper to identify MRSA. They demonstrated that this assay provides a high-sensitivity detection of MRSA after only 3 h of culture time and minimal sample processing [114]. In addition, MALDI-TOF provided promising results in bacterial subtyping for rapidly detecting biomarkers in 229 S. aureus isolates retrieved from subclinical bovine mastitis [115]. Smith and collaborators developed a novel method for identifying colistin resistance in Enterobacter species and Klebsiella aerogenes without performing antimicrobial susceptibility testing. Firstly, they determined broth MICs for colistin and performed killing assays. Subsequently, they used the novel fast lipid analysis technique for lipid A extraction and further analysis via MALDI-TOF. The correlations between MIC, killing efficacy, and predictive lipid A modifications demonstrate the potential utility of MALDI-TOF as a rapid diagnostic platform for colistin resistance in Enterobacter species [116].

Recently, Flores-Flores and collaborators conducted a study aiming to identify potential biomarker peaks for resistance or biofilm production in ESKAPE pathogens using MALDI-TOF MS. They detected antimicrobial susceptibility and biofilm production properties in carbapenem-resistant A. baumannii, MRSA, P. aeruginosa, VRE, and carbapenem-resistant Enterobacterales strains. However, despite that, they did not find potential biomarker peaks for biofilm production. Several potential biomarker peaks for drug resistance were detected in VRE, MRSA, and P. aeruginosa [117].

Recent studies revealed the utility of MALDI-TOF MS in MRSA detection, colistin resistance profiling, and AMR markers identification in ESKAPE pathogens, with limited results in identifying biofilm-associated biomarkers. Integrating AI-powered systems for spectral analyses is crucial for enhancing its diagnostic accuracy, and it has the potential to revolutionize clinical and veterinary microbiology.

NGS Technology

NGS is an advanced technology used for whole genome sequencing (WGS) of microbial pathogens or for metagenomic sequencing [109], providing valuable information regarding complete genome architecture, genetic varieties, gene expression, and epigenetic mechanisms. Current endeavors in NGS concentrate on expanding sequencing accuracy, diminishing costs, and improving bioinformatic computations, opening new perspectives in the development of personalized medicine [89, 109, 118]. NGS can elucidate the etiology of HAIs, including those that are not culturable by established methods, by analyzing specific ribosomal RNA sequences, such as 16S rRNA for bacteria and 18S RNA and the internal transcribed spacer region (ITS) in fungi [109, 119]. Park and collaborators developed a new NGS panel primer set targeting 18 specific virulence factor genes from six target pathogens (Bacillus cereus, Yersinia enterocolitica, S. aureus, Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus). The NGS panel detected all 18 target genes in a single reaction, yielding almost the same efficiency and specificity as the quantitative real-time PCR (qPCR) analyses [120]. Gaston and collaborators evaluated the performance of a broad targeted NSG panel consisting of a Respiratory Pathogen ID/AMR (RPIP) kit (Illumina, Inc.) with automated Explify bioinformatic analysis (IDbyDNA, Inc.) to identify the AMR markers from bronchoalveolar lavage samples. AMR markers were detected in 136 of 201 samples, and AMR associations were made for various resistant organisms, including ESBL-producing E. coli, VRE, MRSA, and Mycobacterium tuberculosis [121].

In the context of the influence of the COVID pandemic on HAI management, recent studies demonstrated that WGS could be used to enhance clinical and epidemiological investigations, identify cryptic SARS-CoV-2 transmission pathways, and aid IPC teams in integrating clinical, phenotypic, or epidemiological data for enhanced surveillance [122,123,124].

Data-Driven Methodologies

Data-driven methodologies, i.e., artificial intelligence (AI) and machine learning (ML) have become game-changing technologies in the healthcare industry, improving the early detection, prediction, and prevention of HAIs, therefore augmenting patient outcomes and lessening the tension in healthcare systems [125]. Large amounts of clinical, microbiological, and patient data can be processed in real-time by AI and ML algorithms to find early indicators of HAIs. In order to detect abnormalities or patterns suggestive of infections, such as shifts in vital signs (e.g., temperature, heart rate) or laboratory results (e.g., white blood cell counts), AI-powered systems (e.g., automated infection surveillance systems) can examine patient electronic health records (EHRs) [88]. Natural language processing algorithms can extract relevant information from unstructured clinical notes in EHRs, such as symptoms or observations, to flag potential infections [126, 127]. ML algorithms applied to imaging data, such as X-rays or CT scans, can aid in detecting infections like ventilator-associated pneumonia (VAP) [128].

ML aids in analyzing microbial genome sequences to identify virulence factors and resistance genes [129, 130] and can predict future outbreaks by correlating environmental and patient factors with infection patterns [131]. Two recent studies integrated MALDI-TOF MS with ML technologies to evaluate the efficacy of mass spectra for predicting AR and discrimination of vancomycin-susceptible from vancomycin-resistant isolates. They analyzed protein spectra from 178 E. faecium and 2229 S. aureus, E. coli, and K. pneumoniae clinical isolates using classification algorithms like support vector machine, random forest, partial least squares–discriminant analysis (PLS-DA), logistic regression, and CatBoost. The results demonstrated that integrating MALDI-TOF MS with ML technologies could enhance resistance prediction and represent a rapid and effective tool for VRE screening [132, 133].

AI and ML models optimize the allocation of resources, such as staffing and sterilization protocols, to reduce the likelihood of HAIs. AI systems analyze patient flow and room usage to recommend optimized cleaning schedules [134]. Computer vision and AI-powered tools monitor compliance with infection control practices, such as hand hygiene and proper use of personal protective equipment (PPE) [134, 135]. Recent data show that AI and ML can build predictive models to estimate the risk of HAI development for individual patients based on historical and real-time data [136].

Current Progress and Future Perspectives on Alternative Approaches for Combating And Treating HAIs

Recent studies show that the most frequently isolated microorganisms causing HAIs are MDR pathogen, known as ESKAPE or ESCAPE [11, 36, 86]. These MDR pathogens are a significant public health issue in clinical settings, increasing mortality when the initial antibiotic treatment is inappropriate, especially if the patient is infected with bacterial strains resistant to many antibiotics. In conclusion, new prevention and treatment options for these bacterial strains causing HAIs are urgently required. Among the new strategies, phage therapy, vaccination and microbiome-based interventions are promising alternatives to mitigate life-threatening illnesses caused by these bacteria [137,138,139].

Phage Therapy Against HAIs Causative Bacteria

Phage therapy is an emerging option that can offer an alternative to ineffective antibiotic treatments for antibiotic-resistant bacteria causing HAIs. This strategy is based on natural viruses called bacteriophages, which can infect, replicate, and, theoretically, destroy the bacterial population in an infected patient [140].

In 2016, the first successful clinical use of intravenous bacteriophage therapy occurred, treating severe MDR A. baumannii infection. From this point, the interest in bacteriophage therapy renews [141, 142]. Wright and collaborators conducted a randomized, double-blind, placebo-controlled phase I/II clinical trial including 24 patients to evaluate the efficacy and safety of a therapeutic bacteriophage preparation (Biophage-PA) targeting P. aeruginosa in chronic otitis. The patients received either a single dose of Biophage-PA or a placebo. The results showed that P. aeruginosa counts were significantly lower only in the phage-treated group, and no treatment-related adverse event was reported [143]. In another phase 1 clinical trial, the efficiency of a cocktail containing eight bacteriophages (WPP-201) targeting P. aeruginosa, S. aureus, and E. coli was tested in 39 patients with chronic venous leg ulcers who completed the trial. The authors concluded that the percentages of healed participants were not significantly different between the treatment and control groups, and no adverse events occurred [144]. Terwilliger and collaborators reported using a four-phage cocktail to treat urinary tract infections caused by E. coli in a 56-year-old male. The patient tolerated the phage cocktail without any adverse effects, and no bacteria were detected in the urine after the first dose of the phage [145]. The results of the recent clinical trials aiming to use phage therapy targeting HAIs causative bacteria are summarized in Table 1.

Table 1 Clinical trials based on bacteriophage therapy against HAIs causative bacteria
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The results of the clinical studies indicate a variable efficacy of bacteriophage therapy [144, 148, 149]. One reason can be that most clinical trials have different designs, using different bacteriophage variants, treating different conditions (chronic venous leg ulcers, chronic otitis, acute bacterial diarrhea, urinary tract infections) and bacteria (P. aeruginosa, A. baumannii, S. aureus, E. coli, P. mirabilis) and using different concentrations of bacteriophage (Table 1). Subsequently, given these differences, it is troublesome to extract accurate conclusions. However, several clinical trials reported great safety profiles, improvement of clinical signs after the first doses, and decrease of targeted bacteria counts [145,146,147, 150, 152,153,154]. Future clinical trials are needed to test the efficiency of specific bacteriophage strains and the accurate dosage and to enroll more patients caring for different HAIs-causative bacteria.

Harnessing Microbiome and Host–Pathogen Interactions to Mitigate HAIs

Commensal microorganisms, collectively called the microbiome, are essential to host biology, profoundly influencing immune responses and infection susceptibility [155]. The microbiome supports immune system homeostasis and can affect the progression of infections caused by pathogenic agents [156]. A balanced microbiome is fundamental to maintaining host health, protecting against infections through multiple mechanisms, including competition for resources and ecological niches, modulation of immune responses, regulation of epithelial barrier function, interaction with pathogen signaling mechanisms, induction of antiviral responses, and the production of antimicrobial metabolites [156,157,158,159,160,161]. The significance of this role varies depending on the host context, justifying the exploration of microbiota-based therapeutic strategies for HAIs prevention and treatment.

An important proportion of HAIs results from the transition of the microbiota from a balanced state to dysbiosis, increasing susceptibility to opportunistic infections. This alteration is influenced by multiple factors, including hospitalization conditions and reasons, environmental influences (both internal and external), and the hygiene status of the healthcare settings [162, 163]. Therefore, the integrated and multidimensional approach required for controlling HAIs should include microbiota preservation [163, 164].

A well-known and illustrative example is that of C. difficile, an opportunistic, spore-forming, anaerobic, Gram-positive microorganism capable of colonizing the gastrointestinal tract [165]. Although it is considered part of the normal intestinal microbiota, its proliferation is typically suppressed by dominant anaerobic microorganisms. The colonization rate of the human intestine with C. difficile varies with age, being higher in infants and gradually decreasing with age [166, 167]. A critical opponent against the colonization of the intestinal epithelium by C. difficile is represented by the integrity of the intestinal microbiota’s barrier. The disruption of this barrier, whether due to antibiotic administration, leads to the loss of protective microbiota and creates ecological niches that favor C. difficile colonization [168, 169]. In addition to antibiotic exposure, prolonged hospitalization, a low-fiber diet, advanced age, and proton pump inhibitor therapy can contribute to dysbiosis and increase the risk of C. difficile infection. Thus, on the one hand, gut microbiota influences infection susceptibility, while on the other hand, alterations caused by external factors can promote C. difficile proliferation and disease onset [160]. Moreover, dysbiosis can also lead to an exacerbated inflammatory response, promoting intestinal damage induced by C. difficile toxins [157, 170]. Alongside C. difficile, an imbalanced microbiome can facilitate infections with other opportunistic pathogens, such as K. pneumoniae, P. aeruginosa, and E. faecium, frequently involved in HAIs. Therefore, restoring a healthy intestinal microbiome may be an effective strategy for preventing and treating these infections [171].

Various microbiota-based interventions are being studied and clinically applied to prevent and control HAIs. Among the most significant are fecal microbiota transplantation (FMT) and probiotics [167, 172].

FMT is one of the most effective therapies for recurrent C. difficile infections, with success rates exceeding 80% in restoring intestinal microbiome balance. The procedure involves transferring microbiota from a healthy donor to the patient [173]. FMT can be administered orally (in capsule form), via the digestive tract (through nasogastric, nasoduodenal, or nasojejunal tubes), or rectally (via enema or colonoscopy). Each approach has specific advantages and disadvantages. The effectiveness of FMT relies on reintroducing a diverse microbial community that suppresses C. difficile growth through competition for nutrients and the production of antimicrobial metabolites [174].

Additionally, the administration of probiotics, such as Saccharomyces, Lactobacillus, and Bifidobacterium, can help prevent HAIs by colonizing the intestine with beneficial species that inhibit pathogens through various mechanisms. Numerous studies have demonstrated that probiotics can effectively reduce the incidence of C. difficile infections in hospitalized patients undergoing antibiotic therapy [175].

Vaccination Strategies Against HAIs Causative Bacteria

Vaccination is one of the most important approaches in the fight against AMR, which is critical in reducing antibiotic consumption and infection rates with resistant strains [176]. Currently, the efforts are concentrated on exploring novel technologies that can be harnessed to identify and address current challenges impeding advances in antigen and vaccine discoveries [177].

Different research directions in vaccine development are inactivated whole cells (IWC) [178], outer membrane vesicles (OMVs) [179], outer membrane complex (WTO) [180], outer membrane proteins (OMP) including OmpA [181], and passive immunization through monoclonal antibodies (mAbs) [182]. These molecules were evaluated in several clinical trials aiming to discover feasible vaccines against pathogens, especially those from the ESKAPE group which are one of the most prevalent MDR bacteria responsible for HAIs in clinical settings [183,184,185,186,187].

Several preclinical studies investigated the efficiency of vaccines using semi-synthetic glycoconjugates against K. pneumoniae [185], OMPs against P. aeruginosa [187], and a live attenuated A. baumannii strain deficient in thioredoxin against A. baumannii strains [186].

In two clinical trials conducted by the same research group, the authors used a vaccine containing the capsular polysaccharide serotypes 5 and 8 conjugated to the nontoxic mutant form of diphtheria toxin (CRM197), a recombinant mutant clumping factor A (ClfA) and a recombinant manganese transporter C (MntC), named SA4Ag to achieve immunity against S. aureus. The vaccine was well tolerated, inducing antibody synthesis and supporting immune responses 12 months after vaccination [183] and 36 months after vaccination [184] (Table 2).

Table 2 Clinical trials evaluating the efficiency of vaccines targeting HAIs causative bacteria
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Other three clinical trials (NCT02388165, NCT00071214, NCT01160172), including a total of 7138 patients, investigated the efficiency and immunogenicity of a staphylococcal vaccine based on capsular polysaccharides type 5 and 8 (CPS5/8) against S. aureus strains. Levy and collaborators observed staphylococcal vaccine-induced functional antibodies with no safety concerns and robust humoral immune responses [188]. In the double-blind trial conducted by Fattom and collaborators, 3359 patients received the CPS5/8 vaccine, inducing a robust immune response and an acceptable safety profile [189]. More recently, Hassanzadeh and collaborators led a multicenter, double-blind trial in which patients received a single dose of SA4Ag (Table 2). While inducing robust functional immune responses, the vaccine did not exhibit efficiency in preventing postoperative S. aureus infection [190]. Although two studies [188, 189] consistently confirmed the immunogenicity and the favorable safety profile of the SA4Ag vaccine, the recent study by Hassanzadeh and collaborators demonstrates the failure in preventing postoperative S. aureus infections [190]. The results of these clinical trials are summarized in Table 2.

Recently, Fierro and collaborators conducted a study (NCT03819049) showing that the ExPEC10V (VAC52416) vaccine was well tolerated, exhibited a robust antibody-mediated immunogenic response, functional opsonophagocytic killing activity across all measured serotypes, and had a favorable safety profile in participants with a history of UTI (Table 2) [192].

In P. aeruginosa-driven HAIs infection, several trials focused on the evaluation of the safety, immunogenicity, and efficiency of various mAbs (NCT01695343, NCT02696902, NCT03027609, NCT03494959, NCT04763759) and OMP (NCT00876252, NCT01563263) as vaccines for preventing or treating infections caused by this pathogen. These clinical trials are conducted across phases ranging from I to III, involving diverse patient populations, including those with cystic fibrosis, ventilator-associated pneumonia, and burn wounds (Table 2).

The vaccines based on mAbs target specific P. aeruginosa components, such as exotoxins or surface polysaccharides. Several mAbs demonstrate promising results regarding safety and immunogenicity. However, other trials show limited efficacy in clinical settings, mainly due to variability in patient responses (low levels of the type III secretion proteins), and the complexity of the pathogen’s virulence mechanisms [193, 194] (Table 2).

In two clinical trials, (NCT01563263, NCT00876252), the vaccines based on OMP produced a significant immunogenic effect against P. aeruginosa. However, no clinical benefits were registered in terms of mortality and preventing P. aeruginosa infection (Table 2). In conclusion, although OMP-based vaccines have shown potential in eliciting immune responses, their clinical efficacy in preventing P. aeruginosa infections has yet to be firmly established.

Reportedly, no vaccine candidates for A. baumannii have stepped into clinical trials [199,200,201]. One reason could be the easy degradation of subunit vaccines in vivo and weak immunogenicity. Several A. baumannii subunit vaccines have been investigated in vivo regarding immunogenicity and protective effects [202,203,204,205,206]. The most studied components are OMPs (OmpA, Omp33-36, Omp22, OmpW) [207], OMVs, fimbrial proteins (CsuA/B and FimA), capsular polysaccharide [208], and antigens predicted by reverse vaccinology (Pfsr, LptE, OmpH, CarO and FimF) [209]. Choosing the appropriate adjuvants, immunization routes, or delivery vehicles to prepare subunit vaccines can slow down degradation and improve immunogenicity [201].

Future strategies for vaccine development are currently being investigated, including reverse vaccinology [210], systems immunology and serology [211], mass spectrometry-based immunopeptidomics [212], computational protein structure prediction and modeling [213,214,215,216], and computational tools for T cell epitope-based vaccines [177, 217].

Hospital Environment and IPC Measures in HAIs Surveillance

Surveillance of HAIs remains a critical challenge in both resource-rich and resource-limited settings, yet it is essential for informing policymakers and improving IPC strategies. Pathogens associated with HAIs are typically transmitted via two primary routes: airborne (droplet) transmission, occurring during natural processes such as breathing, talking, sneezing, or coughing, and indirect transmission through contaminated surfaces (fomites) [32, 54, 218,219,220]. Certain microorganisms, including MRSA, vancomycin-resistant S. aureus, Clostridioides spp., Pseudomonas spp., Enterococcus spp., and viruses such as SARS-CoV, influenza virus, and norovirus, can persist on surfaces for hours to months, significantly increasing the risk of outbreaks [221, 222].

Up to 40% of HAIs have been attributed to cross-contamination by healthcare workers, where pathogens spread via contaminated clothing, gloves, and frequently touched surfaces such as medical equipment, tables, and beds [220, 223]. The hospital environment itself plays a pivotal role in sustaining and transmitting extended-spectrum beta-lactamase (ESBL)-producing bacteria [224]. Enhanced infection control measures, including the use of UV-C light for surface disinfection, have been shown to reduce HAIs caused by these microorganisms and are regarded as highly effective sanitization strategies [225].

The persistence of pathogens on surfaces is influenced by material properties such as roughness, porosity, electrical charge, and hydrophobicity. Proteins or other biological substances in body fluids (sweat, mucus, saliva) may stabilize these pathogens, prolonging their viability. A documented outbreak of carbapenemase-producing Enterobacteriaceae (CPE) in two hospitals was linked to contamination by floor-cleaning equipment, underscoring the risks associated with inadequate environmental hygiene [226]. Proper disinfection protocols significantly reduce HAIs, as evidenced by research indicating a higher risk of pathogen colonization in patients occupying rooms previously used by individuals infected with MDR bacteria [227]. Adhering to international recommendations for cleaning and disinfection, such as those in the National Infection Prevention and Control Manual (NIPCM) of England, is vital for mitigating infection risks [228].

Recently, a study conducted in a tertiary care hospital aimed to evaluate the biofilm eradication properties of several commercially available disinfectants bleach, including Optizan, Virkon, and Clinell against ESBL-producing bacteria. The authors isolated the ESBL strains from wastewater pipes, determined the antibiotic susceptibility profiles, and assessed their ability to form biofilms. The results showed that all disinfectants displayed strain-dependent biofilm eradication [229].

The European Cooperation in Science and Technology (COST) established the ‘AMiCI—Antimicrobial Coating Innovations to prevent infectious diseases’ action, aiming to investigate the influence of antimicrobial coatings (AMCs), specifically for surfaces in healthcare settings [230]. Recent studies emphasize the need for broad-spectrum antimicrobial coatings to prevent infectious diseases transmission, aligning with recommendations from the ECDC [231]. Novel nitric oxide (NO)-releasing polymeric coatings, designed for medical applications, have demonstrated substantial antibacterial activity against P. aeruginosa and MRSA, achieving complete bacterial reduction within 24 h and significant SARS-CoV-2 elimination within 10 min [32]. Integrating copper-based adhesives with UV-C disinfection has also been linked to reduced HAIs rates and the elimination of ESBL-producing bacterial infections, reinforcing its potential as a key strategy against MDR pathogens [84]. While the antimicrobial properties of copper have been demonstrated, studies assessing its impact on MDR bacterial infections, particularly in neonatal care, remain limited [232, 233]. Preventive applications of copper have shown promise in decreasing infection rates, reducing antibiotic usage, and shortening hospital stays [234, 235]. Copper and silver ion applications have shown promise in disrupting biofilms, decreasing infection rates, reducing antibiotic usage, and shortening hospital stays [230, 234, 235]. Contact-active antimicrobial coatings containing chitosan, quaternary ammonium compounds, polyaniline, and biocide-releasing antimicrobial coatings have exhibited good results in HAIs reduction [220]. Recently, Cheng and collaborators conducted a pilot randomized controlled trial to investigate the effectiveness of an antimicrobial surface coating randomized trial on 96 stretcher rails with the highest touch frequency in an emergency department. They used a modified acrylate and silane, producing biocidal activity against bacterial cell membrane and murein layer. Bacterial isolation (MRSA) was performed pre- and post-treatment at 24 h, 7, and 180 days. The results showed that total aerobic bacteria found on antimicrobial-coated patient transport stretcher rails was significantly lower than placebo rails at 24 h [236].

Approximately 35–50% of HAIs are attributed to five primary healthcare practices: hand hygiene, urinary catheter use, intravenous (IV) devices, pulmonary supports (e.g., ventilation), and surgical procedures. Addressing these aspects can lead to significant improvements in patient safety and infection control [237]. Hand hygiene, a fundamental preventive measure, remains the most effective strategy against HAIs [12]. Historical research by Labarraque, Semmelweis, and Wendell Holmes established the role of hand hygiene in preventing nosocomial infections, highlighting the transmission of pathogens via healthcare workers’ hands [238,239,240]. Proper implementation of hand hygiene protocols, along with protective gown and glove usage, has been shown to reduce HAIs in transplant recipients in pediatric ICUs [241]. A surveillance study aimed to evaluate hand hygiene practices (hand rubbing with alcohol-based hand rubs) in 342 nursing students. The study was based on an electronic questionnaire to gather data regarding hand hygiene after contact with body fluid, before a clean or aseptic procedure, before touching a patient, after touching a patient, and after touching patients’ surroundings. Even though practices were generally positive, 16% of students were unaware of the clinical contraindications for using alcohol-based hand rub, and 9% did not know when to use soap and water or alcohol-based hand rub [242]. Another observational study led by the same research group sent a similar questionnaire to 872 nursing and medical students from one university. They observed higher compliance with the WHO’s ‘My Five Moments for Hand Hygiene’ model among nursing students than medical students. As in the first study, 16% of nursing students were not aware of the clinical contraindications to alcohol-based hand rub [243].

Antibiotic stewardship plays a crucial role in HAIs reduction by preserving the efficacy of existing antimicrobial agents [12]. A notable study found that short-term antibiotic use in cardiac arrest patients significantly decreased ventilator-associated pneumonia incidence [244]. Another study from London, United Kingdom, analyzing pediatric antibiotic prescriptions over five years, revealed that 32.5% of hospitalized children received antimicrobial agents, predominantly from the "Watch" category (46.8–70.5%), highlighting the urgent need for stewardship initiatives to optimize prescribing and combat AMR [245]. Even in the Group of Seven (G7) nations (Canada, France, Germany, Italy, Japan, the United Kingdom, and the United States), IPC measures, education programs, and environmental pollution control (e.g., antibiotic and pesticide emissions) require further reinforcement to combat AMR effectively [246].

To enhance IPC practices, the RISK PRINCIPE research project aims to integrate patient data from diverse sources to develop infection risk profiles and validate a semi-automated surveillance system for hospital-acquired bloodstream infections. This platform will automate infection case registration and facilitate the early identification of vulnerable patient groups for targeted interventions [247].

Overall, a combination of IPC protocols, enhanced surface disinfection, prudent antibiotic stewardship, and rigorous surveillance systems could significantly reduce HAIs and curb the spread of AMR. Future research should prioritize the development of innovative materials for infection control and continue strengthening global IPC strategies to enhance patient safety.

The Link Between Climate Change, AMR, and HAIs

One Health is an integrated and collaborative strategy aiming to contribute to sustainable development and solve problems related to water, food, energy, and climate change [248]. The intricate interconnection between human, animal, and environmental health forms the cornerstone of the One Health multidisciplinary concept, addressing complex global health challenges including HAIs and AMR. It is well known that climate change acts as a catalyst for the emergence and spread of infectious diseases. Rising temperatures, altered precipitation patterns, and extreme weather events contribute to the geographical redistribution of pathogens and vectors, while also impacting water and air quality. These environmental shifts can exacerbate the prevalence of HAIs by straining healthcare infrastructure, increasing patient vulnerability, and facilitating the proliferation of resistant organisms. Simultaneously, climate-induced changes in ecosystems can further influence the spread of resistant bacteria across different sectors. The increased incidence of HAIs in the context of climate-related disasters and resource-limited settings underscores the urgent need for comprehensive strategies that address both environmental and healthcare factors.

Recent studies suggest that temperature rise due to climate crisis could impact AMR expansion in humans, animals, plants, and the environment [249, 250], due to association with increased bacterial growth rates and horizontal gene transfer [248, 251] (Fig. 3). Several studies demonstrated the link between high-temperature climates and the rise of heavy metals or biocides concentrations in soil and water, influencing AMR by co-resistance mechanisms [27,28,29,30,31,32].

Fig. 3
Fig. 3
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Environmental changes connected with HAIs expansion. Temperature rise is linked with increased bacterial growth rates and heavy metals or biocides concentrations in soil and water, influencing AMR by co-resistance mechanisms. In addition, wastewater, healthcare and industrial facilities can lead to water pollution by antibiotic, microplastic, pesticide and toxic metals emission, influencing HAIs expansion (created with Adobe Illustrator CS6, Adobe Photoshop CS3)

An investigation of AMR drivers and pathways in surface waters revealed that HAIs are influenced mainly by wastewater, healthcare facilities, agricultural settings, food, wildlife populations, and climate change [252]. Starting from over 900,000 clinical isolates retrieved from several clinical settings in 30 European countries, Kaba and collaborators conducted a cross-sectional study to decode the link between HAIs causative bacteria and environmental factors. The reported connection between carbapenem-resistant P. aeruginosa, K. pneumoniae, E. coli, and MRSA strains and warm-season changes in temperature (32–36 °C) support the impact of climatic factors on AMR [253]. Similarly, Macfadden and collaborators reported the correlation between the AMR in E. coli, K. pneumoniae, and S. aureus and the 10 °C difference in average temperature across regions of the US, association consistent across most classes of antibiotics and pathogens [28].

Other findings show that climatic conditions (dew point, humidity) are linked to the severity of respiratory infections among hospitalized children [254, 255].

De Jongh and colleagues recently suggested that honeybees be used as a model organism to better explain the interactions between climate change and AMR based on the One Health perspective. They identified three potential liaisons between environmental pollution and climatic factors and the risk of AMR. Firstly, the AR achieved by honey bee cells through MDR transport upregulation could extend the risk of AMR in symbiotic microbes. Secondly, they found that cell membrane transporters could diminish microbial exposure to the antimicrobial agents administered. Thirdly, a decrease in honey bee immunity could influence the quick spread and pathogens development inside the hive [256].

These findings are an important step in understanding the relationships of AMR with climate change and environmental pollution in the context of One Health. Adopting the One Health approach allows for more effective management of zoonotic and vector-borne diseases and supports the development of health infrastructures that are resilient to climate change and natural disasters. Therefore, this approach could improve disease prevention strategies and address health inequities, facilitating the construction of stronger, safer, and more equitable health systems adapted to global challenges [22]. In health systems, constant monitoring and effective international cooperation policies are essential for reducing the risks associated with climate change [257].

Although studies highlight multiple ways climate change and AMR may intersect and influence each other, research in this area is still in its infancy, with few papers focusing on the intersection of the two topics. Greater attention, based on empirical evidence, is needed to explore knowledge gaps related to the specific risks associated with climate change and MDR bacteria, including fungi, helminths, protists, and viruses [24, 250].

Conclusions: Main Findings and Future Directions

This review aimed a holistic approach to HAIs by covering: i) their microbial determinants (pathogens involved, prevalence, AR, microbiome disruptions, rapid diagnosis tools, alternative therapeutic and prophylactic strategies); ii) the role of hospital environment (focusing on contamination, infection control strategies, and transmission pathways); iii) climate change (impact on pathogen spread, hospital hygiene challenges, and AMR evolution).

Main Findings

  • The studies dealing with HAIs prevalence demonstrate that while high-income countries report lower prevalence rates (< 10%), low- and middle-income countries exhibit higher rates (up to > 20%), often due to inadequate surveillance and infection prevention measures.

  • Although several high-income countries have made advancements in cutting-down HAIs’ negative consequences by implementing molecular diagnosis tools, stringent infection control policies and statistical modeling, there are still shortcomings in regions facing infrastructural and financial constraints [54].

  • Factors like inappropriate antibiotic use, prolonged hospitalization, and environmental parameters changes can lead to dysbiosis, favoring the rise of opportunistic pathogens like P. aeruginosa, K. pneumoniae, and C. difficile.

  • Phage therapy is an emerging option that can offer an alternative to ineffective antibiotic treatments for antibiotic-resistant bacteria causing HAIs. Although early clinical trials reveal favorable safety profiles and microbiological activity, the discrepancies in study design, bacterial targets, and phage formulations do not allow the formulation of indisputable conclusions, underscoring the need to optimize phage selection and standardize dosages.

  • Clinical trials dealing with vaccine development for MDR bacteria have yielded conflicting results. Although several candidates, like SA4Ag and ExPEC10V conjugates, have provided consistent pharmacokinetic profiles, their clinical efficacy in preventing infections remains questionable. For instance, vaccines against K. pneumoniae, P. aeruginosa, and S. aureus exhibited low efficiency due to pathogen complexity and host variability. In addition, subunit vaccine stability and immunogenicity shortcomings have stopped the progress of A. baumannii vaccines into clinical trials.

  • Recent advances in microbiome research have spurred interest in therapeutic interventions aimed at restoring microbial balance. Two promising strategies, FMT and probiotic therapy, proved highly effective against recurrent C. difficile infections and have been shown to reduce HAI incidence in hospitalized patients undergoing antibiotic therapy [167, 172].

  • AI and ML offer promising predictive capabilities in processing large volumes of clinical, microbiological, and patient data but require robust data integration. Logistical, ethical, and economic constraints must be addressed to accomplish and adopt a multidisciplinary approach.

Future Directions

  • By integrating preventive and therapeutic strategies based on biological factors (e.g., vaccination, phage therapy or microbiome-based strategies) into HAIs prevention and treatment protocols, healthcare systems may reduce reliance on antibiotics and lower infection rates.

  • Advances in metagenomics and AI may allow patient-specific microbiome assessments to identify those at high risk for HAIs.

  • In the era of the climate crisis, life-threatening infectious diseases could still be reduced by implementing One Health strategies and recognizing the intimate connection between human health, animals, and the environment.

To conclude, HAIs are still a demanding global challenge, requiring stringent IPC policies, computer vision, and AI-powered tools. Despite promising avenues like integrated One Health approaches, optimized phage therapy, microbiome-based interventions, and targeted vaccine development, several knowledge gaps in clinical efficacy, standardization, and pathogen complexity remained to be answered.