The review included accessible full-text original articles published in English before March 15, 2023, without any restrictions on the publication year of the included studies. In addition, the systematic review included clinical studies, case reports, environmental and one-health approach studies that investigated the antimicrobial resistance genes in K. pneumoniae in the GHC countries using phenotypic and genotypic methods. All studies that addressed MDR K. pneumoniae, including ESBL, carbapenemase-producing and colistin-resistant strains, were included as a sub-population of Enterobacterales. In contrast, all studies reporting antimicrobial resistance mechanisms in K. pneumoniae using phenotypic detection methods were excluded from this review. Additional exclusion criteria included reviews, conference abstracts, study protocols, and studies performed outside the GHC countries.

All references of extracted studies were imported to EndNote (version 21.2), where duplicates were removed. Two stages of screening were performed by two independent reviewers. The first screening stage included title and abstract screening of the imported references. Afterwards, all studies that were included during the first stage of screening underwent full-text screening during the second stage. The decision of each reviewer was taken blindly, and disagreements between researchers were resolved through discussion with a third reviewer. Following the two screening stages, all articles included were carried out for data extraction based on a data collection form designed to address the aim of the current review (Supplementary Table S1) using a Microsoft Excel worksheet. The data extracted from each study included the following: the citation, the country where the study was performed, the study type, the study period in months, the sample size, the specimen sources, the genotypic detection method, detected antimicrobial resistance genes, detected multilocus sequence types, and the year(s) of specimen collection.

The quality of each article included in the review was assessed by two independent reviewers using the National Heart, Lung, and Blood Institute (NIH) Study Quality Assessment tools adapted for each study’s design.³ Two tools were used: (1) the NHLBI Quality Assessment Tool for Observational Cross-Sectional Studies and (2) the NHLBI Quality Assessment Tool for Case Series Studies. The quality of each study was rated as good, fair, or poor to assess the risk of bias in the study due to flaws in study design or implementation (Supplementary file S2).

Due to the nature of the current systematic review, the results are presented as frequencies and percentages. Microsoft Excel was used for the quantitative analysis of the extracted data. The study period was presented as mean ± SD. The number of studies in each country and the prevalence of antimicrobial resistance genes were presented in frequencies. GraphPad Prism (version 10.2.3) (347) was used to create graphs and figures.

A comprehensive systematic literature search was conducted to identify relevant studies on MDR of K. pneumoniae in the Arabian Peninsula. The search yielded a total of 1,663 studies, which were imported into the EndNote software (version 21.2). After removing duplicate studies (n = 1,039), the titles and abstracts of 624 studies were reviewed for possible inclusion in the current review. Out of 624 studies, 531 were excluded due to their irrelevance to the scope of the review. The remaining 93 studies were assessed for eligibility through full-text screening. Consequently, 26 articles were excluded for reasons detailed in Figure 1. Hence, a total of 67 articles met the eligibility criteria and were included in the present review.

The quality assessment results of the 67 included studies are presented in Supplementary Table S1 based on the NHLBI study quality assessment tools for observational cross-sectional studies (Supplementary Table S1A) and case series studies (Supplementary Table S1B). The NHLBI Quality Assessment Tool for Observational Cross-Sectional Studies was used for only two studies, both of which were classified as fair quality (Moghnia et al., 2021a; Sonnevend et al., 2022). Most studies were evaluated using the NHLBI Quality Assessment Tool for Case Series Studies. Out of 67 studies, 37 (55.2%) were classified as good quality, while 30 (44.7%) were classified as fair quality, as cited and described in detail in Supplementary Table S1. None of the 67 evaluated studies were classified as poor quality.

Out of the 67 included studies, Saudi Arabia contributed more than 60% (41/67), followed by Kuwait and the UAE, with seven and six studies, respectively. Oman and Qatar contributed four studies in each country, while Bahrain contributed only three studies. Furthermore, researchers conducted four studies using samples collected from various countries in the area (Al-Baloushi et al., 2018; Sonnevend et al., 2015; Zowawi et al., 2014; Mouftah et al., 2021). Studies of MDR K. pneumoniae in the GHC countries, including ESBL, carbapenemase-producing and colistin-resistant strains, were conducted over an average period of 18 ± 19 months between 2006 and 2021, as shown in Figure 2. The most extended study, which was conducted over 96 months in Saudi Arabia, was on the genetic characterization of colistin-resistant isolates (Okdah et al., 2022). Most of the studies (50.7%) focused on carbapenem-resistant K. pneumoniae (CRKP), followed by ESBL-producing K. pneumoniae (29.8%), as shown in Supplementary Table S2.

Furthermore, all studies were related to clinical settings, while only one study was conducted on livestock/animal samples (Sonnevend et al., 2022), and one study focused on collecting samples from the community (Moghnia et al., 2021a). The predominant specimen sources reported in the majority of studies were urine, sputum, and blood, as shown in Figure 3. The most commonly used genotypic method was PCR, followed by multiplex PCR and the WGS, as detailed in Figure 4.

An extensive analysis of the studies revealed a predominant focus on MDR K. pneumoniae, including ESBL, carbapenemase-producing, and colistin-resistant strains. Among the ESBL genes, bla_CTX-M was identified as the most prevalent, with two variants, bla_CTX-M-14 and bla_CTX-M-15, reported in most studies. The bla_OXA gene was the most identified carbapenemase gene, with bla_OXA-23, bla_OXA-48, bla_OXA-181, and bla_OXA-232 as the most common variants. However, the distribution of these predominant genes varies between the GHC countries, with certain genes reported exclusively in specific countries. This variation is likely due to the differing number of studies conducted in each country, which influences the detection and reporting of particular genes. For instance, while bla_CTX-M-15 was the most predominant ESBL gene in the GHC countries, bla_CTX-M-14 was reported only in Saudi Arabia, Kuwait, and Qatar. Moreover, bla_SHV-1 was reported in Saudi Arabia (Tawfik et al., 2011; Uz Zaman et al., 2014; Al-Qahtani et al., 2014; Alghoribi et al., 2020) and Kuwait (Jamal et al., 2015), while bla_SHV-28 was identified in the UAE (Alfaresi et al., 2011), Qatar (Eltai et al., 2020), and Oman (Poirel et al., 2011). For carbapenemase genes, bla_OXA and bla_NDM were identified in all GHC countries, with varying distributions of their variants across different countries. Conversely, bla_KPC was reported in all countries except Bahrain (Alraddadi et al., 2022; Sonnevend et al., 2022; Abid et al., 2021; Mouftah et al., 2021; Alghoribi et al., 2020; Balushi et al., 2022; Moghnia et al., 2021b; Moghnia and Al-Sweih, 2022; Azim et al., 2019; Al-Tawfiq et al., 2022; Alshahrani et al., 2022), with bla_KPC-2 being the most frequently reported variant. Notably, bla_KPC-2 was first reported in Saudi Arabia (Alghoribi et al., 2020). Additionally, the carbapenemase gene bla_IMP was reported only in Saudi Arabia (Alraddadi et al., 2022; Azim et al., 2019; Ejaz, 2022; Badger-Emeka et al., 2021).

Furthermore, resistance to aminoglycosides and fluroquinolones has also been observed in ESBL- or carbapenemase- producing K. pneumoniae in GHC countries. Among aminoglycoside-resistance genes, aac(6′)-lb was the most frequently identified (Al-Baloushi et al., 2018; Shibl et al., 2012; Abdalhamid et al., 2017; Al-Agamy et al., 2019; Vali et al., 2015), followed by armA and rmtB (Sonnevend et al., 2022; Okdah et al., 2022; Alghoribi et al., 2020; Abdalhamid et al., 2017; Al Sheikh et al., 2014; Abdalhamid et al., 2017; Sonnevend et al., 2013). These genes have been documented in Saudi Arabia, the UAE, Kuwait, and Oman. However, no aminoglycoside-resistance genes were reported in Qatar and Bahrain. Among the fluoroquinolone-resistance genes, qnrB was reported in Saudi Arabia (Okdah et al., 2022; Shibl et al., 2012; Abdalhamid et al., 2017; Al-Agamy et al., 2019; Al-Agamy et al., 2018) and the UAE (Sonnevend et al., 2013), while qnrS was identified in Bahrain (Shahid et al., 2022) and Oman (Balushi et al., 2022). Interestingly, Kuwait stands out, as a study conducted there identified all three key fluoroquinolone-resistance genes: qnrA, qnrB, and qnrS (Vali et al., 2015). Moreover, a study conducted in Saudi Arabia identified a wide array of antimicrobial resistance genes, including aadA2, ant(3′)-lh, armA, sat-A, AmpH, aac(3′)-la, aph(3′)-Vib, strAB, oqxA, msr(E), catA, catB, sul1, tet (WHO Bacterial Priority Pathogens List, 2024), tet(A), tet(D), mcr-1, and dfrA (Al-Baloushi et al., 2018; Okdah et al., 2022; Alghoribi et al., 2020; Abdalhamid et al., 2017). Additionally, other resistance mechanisms were observed, such as mutations in gyrA, ParC, mgrB, PmrA, and PmrB (Alghoribi et al., 2020; Abdalhamid et al., 2017). Structural and functional alterations in outer membrane proteins and efflux systems, including OmpK35, OmpK36, mdtK, tolC, and acrAB (Lagha et al., 2021), were also reported. The presence of multiple resistance mechanisms, in addition to ESBL or carbapenem resistance, classifies these isolates as MDR K. pneumoniae, as they demonstrate resistance to at least one antibiotic from three or more different classes. These findings underscore the multifaceted nature of antimicrobial resistance in the region and the importance of monitoring both genetic and phenotypic mechanisms to understand resistance trends comprehensively.

Alarmingly, colistin-resistant K. pneumoniae has been documented in three studies conducted in GHC countries. Chromosome-mediated colistin resistance, driven by mgrB mutations, was identified in two studies from Saudi Arabia (Okdah et al., 2022; Zaman et al., 2018). Additionally, plasmid-mediated colistin resistance associated with the mcr-1 gene was reported in two studies, one from Saudi Arabia (Okdah et al., 2022) and the other from the UAE (Sonnevend et al., 2022).

The presence and absence of various antimicrobial resistance genes across different GHC countries are shown in Figure 5. Even though many studies did not include the analysis and identification of K. pneumoniae sequence types, some studies reported the presence of specific K. pneumoniae sequence types among their isolates. As some sequence types were reported in different geographical regions, such as ST11, ST14, ST15, ST37, ST101, ST147, ST307, ST340, ST383, and ST2096, other sequence types were specific to some regions, among others, as illustrated in (Figure 6).

The Kingdom of Saudi Arabia contributed the majority of the data from the GHC countries, with a total of 41 studies (61.1% of the total) included in this review conducted between 2010 and 2022. Most studies utilized multiplex PCR to detect ESBL and carbapenem-resistance genes, while a subset of studies incorporated WGS in their methodology. The studies demonstrated that the ESBL gene (bla_CTX-M) was the most predominant resistance gene over the years, followed by β-lactamase genes (bla_TEM and bla_SHV)_, regardless of the variants. Additionally, various carbapenemase genes were detected in Saudi Arabia, including bla_OXA-48, bla_NDM-1, bla_KPC-2, bla_VIM, and bla_IMP. However, bla_OXA-48 and bla_NDM-1 emerged as the most prevalent genes over the years. In 2013 (Shibl et al., 2013), A. Shibl and his team reported bla_OXA-48 and bla_NDM-1 for the first time in Saudi Arabia, while bla_KPC was reported for the first time in 2019 by N. Azim and collaborators (Azim et al., 2019). In 2019, M. Khan reported the presence of triple co-producing carbapenemase genes (bla_OXA-48, bla_NDM-1, and bla_KPC) in 80% of isolates collected from clinical samples using PCR methods (Khan et al., 2019). However, these results have not been subsequently confirmed, indicating the need for further investigation. In contrast, the triple co-producing carbapenemase genes (bla_OXA-48-like, bla_NDM-1, and bla_KPC) were identified in 1.4% of isolates in another study by A. Alshahrani and others in 2022 (Alshahrani et al., 2022). A combination of three carbapenemase genes (bla_OXA-48, bla_NDM-1, and bla_VIM) was reported in 21.7% of clinical isolates, while a combination of four carbapenemase genes (bla_OXA-23, bla_OXA-48, bla_NDM-1, and bla_VIM) was reported in a single clinical isolate in 2022 by R. Booq and the team (Booq et al., 2022). The emergence of ESBL and carbapenemase genes has been well-documented in Saudi Arabia. However, the use of colistin as a last-line treatment has led to the alarming emergence of colistin resistance in clinical isolates of K. pneumoniae. Multiple studies have reported colistin-resistant K. pneumoniae in clinical settings, with chromosomally mediated resistance primarily due to mutations in the mgrB, pmrA, pmrB, and phoQ genes. Furthermore, plasmid-mediated colistin resistance has been identified by acquiring the mcr-1 gene (Okdah et al., 2022; Zaman et al., 2018). The molecular typing results of K. pneumoniae isolates revealed that the most predominant clonal group is clonal complex 14 (CC14), which includes the sequence types ST14 and ST2096 in a study conducted in 2020 and 2022 (Okdah et al., 2022; Khdary et al., 2020). Several studies have analyzed the MLST of K. pneumoniae isolates, identifying various sequence types. Additionally, other sequence types reported in the literature include ST11, ST23, ST37, ST147, ST307, ST340, and ST383 (Al-Baloushi et al., 2018; Sonnevend et al., 2015; Okdah et al., 2022; Uz Zaman et al., 2014; Alghoribi et al., 2020; Al-Agamy et al., 2019; Zaman et al., 2018; Moglad et al., 2022; Uz Zaman et al., 2018; Almogbel et al., 2021). The predominance of CC14 highlights its significance in the epidemiology of K. pneumoniae in Saudi Arabia. Identifying these sequence types underscores the genetic diversity of K. pneumoniae strains circulating in clinical settings, contributing to the complexity of managing infections caused by this pathogen.

The United Arab Emirates (UAE) contributed the third-highest number of studies, following Saudi Arabia and Kuwait, with a total of six studies out of 67 (8.9%). Most of these studies focused on investigating AMR on clinical samples (Sonnevend et al., 2022; Alfaresi et al., 2011; Sonnevend et al., 2013; Sonnevend et al., 2017; Zowawi et al., 2015), with only one study conducted on livestock origin samples (Sonnevend et al., 2022). The majority reported ESBL-producing K. pneumoniae or CRKP, with one study highlighting the presence of colistin-resistant K. pneumoniae in a sample of livestock origin (Sonnevend et al., 2022). In addition, most clinical samples were recovered from various infection sites, including urine, blood, respiratory, and wound swabs. At the same time, the livestock origin specimens are comprised of fecal samples collected from birds in poultry farms. Various resistance genes were reported in the UAE, including β-lactamase genes bla_TEM-1 (Sonnevend et al., 2017) and bla_SHV-11 (Sonnevend et al., 2013) and ESBL genes bla_SHV-12 (Sonnevend et al., 2022; Sonnevend et al., 2013), bla_SHV-28 (Alfaresi et al., 2011), bla_SHV-36 (Zowawi et al., 2015), and bla_CTX-M-15 (Sonnevend et al., 2022; Alfaresi et al., 2011; Sonnevend et al., 2013; Sonnevend et al., 2017; Zowawi et al., 2015), with bla_CTX-M-15 identified as the most predominant ESBL gene in the UAE. Carbapenemase genes were reported in four studies, including bla_OXA-48 (Sonnevend et al., 2022), bla_OXA-181 (Sonnevend et al., 2017; Zowawi et al., 2015), bla_NDM-1 (Sonnevend et al., 2022; Sonnevend et al., 2013), bla_NDM-5 (Sonnevend et al., 2017), and bla_KPC (Sonnevend et al., 2022). Notably, colistin-resistant K. pneumoniae was reported in several studies within the time frame of this literature review. Chromosomal mutations were detected in clinical samples, specifically in the genes mgrB, phoP, phoQ, pmrA, and pmrB (Sonnevend et al., 2022; Sonnevend et al., 2017). The mcr-1 gene, on the other hand, was identified in fecal samples collected from birds in poultry farms (Sonnevend et al., 2022). However, no mcr genes were found in the colistin-resistant K. pneumoniae strains subjected to WGS from clinical samples. MLST analysis in the UAE indicated ST14 was the most predominant sequence type, followed by ST147 and ST231 (Sonnevend et al., 2022; Al-Baloushi et al., 2018; Sonnevend et al., 2015; Sonnevend et al., 2013; Sonnevend et al., 2017; Zowawi et al., 2015). Additional studies reported the detection of various sequence types in the UAE, including ST11, ST231, ST307, ST340, ST383, and ST1318 (Sonnevend et al., 2022; Sonnevend et al., 2022; Al-Baloushi et al., 2018; Sonnevend et al., 2015; Sonnevend et al., 2013).

Kuwait contributed the second-highest number of studies, following Saudi Arabia, with a total of seven studies reporting the ESBL producing K. pneumoniae (Vali et al., 2015; Al Sweih et al., 2011; Dashti et al., 2010), or CRKP (Jamal et al., 2015; Moghnia et al., 2021b; Moghnia and Al-Sweih, 2022; Jamal et al., 2013). Most studies were conducted on clinical samples, with only one study focusing on healthy food handlers from community settings (Moghnia et al., 2021b). In 2008, a β-lactamase gene (bla_TEM-1) and an ESBL gene (bla_CTX-M-15) were identified in all 14 isolates of ESBL-producing K. pneumoniae over a period of 2 months (Al Sweih et al., 2011). Genotypic studies from Kuwait revealed bla_TEM-1 and bla_SHV-11 as predominant β-lactamases genes, while bla_CTX-M-15 was identified as the predominant ESBL genes in ESBL-producing K. pneumoniae. Interestingly, one study showed an outbreak reporting a number of isolates that were phenotypically resistant to cephalosporin antibiotics. Molecular genetics analysis showed that these isolates harbor bla_SHV-112 gene, which is classified as an ESBL genes (Dashti et al., 2010). Moreover, several studies have reported the major carbapenemase genes, which include bla_OXA-48, bla_OXA-181, bla_OXA-232, bla_NDM-1, and bla_KPC-2 (Jamal et al., 2015; Moghnia et al., 2021b; Moghnia and Al-Sweih, 2022; Jamal et al., 2013). Notably, other bla_KPC variants, including bla_KPC-18 and bla_KPC-29, were first identified in Kuwait from community samples between 2016 and 2018 (Moghnia et al., 2021a). The detailed list of all ESBL and carbapenemase genes is presented in Supplementary Table S2. Results of MLST analysis of K. pneumoniae isolates obtained from food handlers reported various sequence types composed of ST10, ST38, ST295, ST1415, and ST1876 (Moghnia et al., 2021b). In addition, three new CRKP sequence types (ST1592, ST1593, and ST1594) were reported in a study conducted between 2011 and 2013 on clinical samples (Jamal et al., 2015). Other sequence types were identified in different studies including ST16, ST25, ST37, ST107, ST485, ST677, ST3495, and ST4743 (Jamal et al., 2015; Moghnia and Al-Sweih, 2022). However, all identified STs in Kuwait were reported as singleton with no observed predominance.

Four studies were conducted in Qatar to detect ESBL and carbapenemase genes in K. pneumoniae isolates obtained from clinical samples such as urine, blood, respiratory, and wound swabs (Abid et al., 2021; Eltai et al., 2020; Perez-Lopez et al., 2020; Pérez-López et al., 2021). These major resistance genes were the most predominant genes in all studies conducted in Qatar between 2015 and 2019 (Eltai et al., 2020; Perez-Lopez et al., 2020; Pérez-López et al., 2021). A study conducted from 2014 to 2017 reported the presence of bla_OXA-48, bla_OXA-181, bla_OXA-232, bla_NDM-1, bla_NDM-5, bla_NDM-7, bla_KPC-2, bla_KPC-3 and bla_VIM-2. In virous sequence types, including ST11, ST147, ST231 and ST383 of which ST147 being the most predominant (Abid et al., 2021). Additionally, co-occurrence of resistance genes was observed, including combinations such as (bla_OXA-48 and bla_NDM-5), (bla_OXA-181 and bla_NDM-1), and (bla_OXA-181 and bla_NDM-5) and (bla_NDM-1 and bla_KPC-3) (Abid et al., 2021). Other studies confirmed the presence of bla_OXA-48, bla_NDM-1, and bla_NDM-5 as the most widely disseminated carbapenemase genes in Qatar (Eltai et al., 2020; Perez-Lopez et al., 2020; Pérez-López et al., 2021). The analysis highlighted bla_OXA-48 and bla_NDM-1 as the dominant carbapenemase genes identified in the country. The molecular typing of K. pneumoniae isolates resulted in the identification of different sequence types through several studies over the years. For instance, a study between 2015 and 2019 identified the following sequence types: ST11, ST25, ST147, ST231, ST383, ST716, ST792, and ST2096 (Eltai et al., 2020), while a study in 2018 reported the presence of ST45, ST268 and ST307 K. pneumoniae sequence types (Perez-Lopez et al., 2020). Other sequence types were identified between 2018 and 2020, composed of ST14, ST17, and ST73 (Pérez-López et al., 2021).

Four studies in Oman were eligible to be included in the current systematic review (Poirel et al., 2011; Balushi et al., 2022; Potron et al., 2011; Dortet et al., 2012). These studies employed molecular methods to investigate the presence of antimicrobial resistance genes in K. pneumoniae, primarily using PCR as the genotypic method. However, only one study incorporated WGS to further elucidate these characteristics (Balushi et al., 2022)^. These studies were conducted in 2011, 2012, and 2022 focused on either K. pneumoniae or CRKP. Studies have reported resistance mechanisms associated with the β-lactamase gene (bla_SHV) and ESBL gene (bla_CTX-M), which were identified as the predominant resistance mechanisms. These studies also identified significant carbapenemase genes, including bla_NDM-1 in 2011, 2012, and 2022 (Poirel et al., 2011; Balushi et al., 2022; Dortet et al., 2012), and bla_KPC-2 in 2022 (Balushi et al., 2022). Additionally, the co-occurrence carbapenemase genes, specifically bla_OXA-181 and bla_NDM-1, were observed in 2012 by L. Dortet and colleagues (Dortet et al., 2012). Furthermore, MLST analysis across all studies in Oman identified ST11 and ST147 as the major sequence types (Al-Baloushi et al., 2018; Sonnevend et al., 2015; Balushi et al., 2022; Potron et al., 2011; Dortet et al., 2012). These sequence types were the most predominant in the region, highlighting their significant role in the epidemiology of K. pneumoniae. Other sequence types reported as singletons include ST14, ST15, ST101, ST340, ST372, ST753, and ST754 (Poirel et al., 2011; Balushi et al., 2022).

Three studies were conducted in Bahrain to evaluate the presence of antimicrobial resistance genes in K. pneumoniae obtained from clinical samples, with notable time gaps between these three studies (Shahid et al., 2022; Bindayna and Murtadha, 2011; Shahid et al., 2014). The first study investigated the prevalence of ESBL-producing K. pneumoniae over 6 months. This study analyzed clinical samples, including urine, blood, respiratory, and wound swabs, and found that nearly all samples tested positive for ESBL. The most prevalent ESBL gene identified was bla_CTX-M (90%), followed by β-lactamase genes bla_TEM and bla_SHV (80%). An important finding was the co-occurrence of these genes, with 70% of isolates harboring all three (bla_TEM, bla_SHV and bla_CTX-M) and only 10% containing just bla_SHV and bla_CTX-M (Bindayna and Murtadha, 2011). The second study reported the prevalence of ESBL-producing K. pneumoniae over 7 months, analyzing clinical samples that included urine, blood, respiratory, and wound swabs. All the K. pneumoniae samples in this study tested positive for the presence of the bla_CTX-M-15 gene (Shahid et al., 2014). The third study, conducted over 7 months, focused on detecting CRKP in clinical samples, with blood being the most common sample type, followed by urine and respiratory. The study identified multiple carbapenemase genes, including bla_OXA-23, bla_OXA-48, bla_OXA-51 and bla_NDM-1. Additionally, some isolates co-produced multiple carbapenemase genes, revealing double or triple carbapenemase gene combinations, including bla_OXA-48, bla_OXA-51 and bla_NDM-1. Notably, 100% of the isolates in this study harbored the qnrS gene alongside multiple carbapenemase genes, contributing to the multidrug-resistant profile (Shahid et al., 2022).