Environmental sampling reveals reservoirs of antimicrobial resistance in a tertiary care Indian hospital: an observational study to strengthen infection control practices

Antimicrobial resistance (AMR) is a global public health problem, which presents a huge threat to the treatment of all forms of bacterial infections. A wide range of bacterial pathogens across the globe are increasingly developing resistance to multiple classes of antimicrobial agents rendering the agents concerned ineffective for the treatment of infections. Bloodstream infection (BSI) and other bacterial infections in sub-Saharan Africa (SSA) and Malawi in particular, are a common cause of morbidity and mortality. Few facilities in SSA however, are able to conduct long-term surveillance and as such the full burden of drug resistant infection (DRI) remain largely unknown across the region. In this thesis, blood cultures routinely taken from adult and paediatric medical patients admitted to Queen Elizabeth Central Hospital (QECH) in Blantyre, Malawi between 1998 and 2016 were analysed to describe trends in BSI and AMR. The analysis revealed a significant decline of BSI in all major pathogens except S. Typhi. However, the majority of isolates were resistant to the Malawian first-line antimicrobial agents (ampicillin, cotrimoxazole and chloramphenicol). Resistance to all the first line antimicrobial agents was more common in Gram-negative pathogens than Gram-positive pathogens. Non-Salmonellae Enterobacteriaceae that produced extended spectrum beta-lactamase (ESBL) and were fluoroquinolone-resistant were detected, and the proportions of these isolates rose significantly during the surveillance. In contrast, a majority of common Gram-positive pathogens remain susceptible to either penicillin or chloramphenicol. Methicillin resistant S. aureus was first reported in 1998 but became regularly detected in the later years of the surveillance. The analysis of blood culture isolates identified E. coli as one of the common causes of BSI in Blantyre, and the proportion of these isolates that were ESBL producers increased over time. Globally, efforts to treat E. coli infections are increasingly being compromised by the rapid, global spread of ESBL-producing E. coli. In this thesis, a whole genome sequencing (WGS) study was carried out to investigate the genetic population structure and molecular determinants of AMR in E. coli isolates from Malawi. Whole genomes of clinical E. coli isolates from patients admitted to QECH were sequenced and analysed using phylogenetic methods and comparative genomics. It was revealed that the E. coli population in Malawi is highly diverse with isolates belonging to five phylogroups, corresponding to five isolate sequence clusters (SCs) that contained over forty sequence types (STs). A unique sub-lineage of ST131 was identified that was distinct from previously defined sub-lineages of this globally disseminated ST. The most common ESBL gene was blaCT X-M-15. Unlike in other settings where presence of the blaCT X-M-15 gene was strongly linked to ST131, here the gene was not lineage-specific suggesting a distinct genomic landscape of ESBL-producing E. coli in Malawi. This thesis also identified Klebsiella spp. isolates as a common cause of BSI in Blantyre, and an increasing proportion of ESBL-producing and fluoroquinolone resistant isolates were identified. The molecular mechanisms and clones of K. pneumoniae associated with ESBL production and fluoroquinolone resistance were yet to be explored in Malawi. Here, a number of K. pneumoniae isolates were selected for WGS, and placed in a global context by comparison with previously sequenced K. pneumoniae isolates from multiple locations outside SSA, in order to identify the molecular determinants of AMR and determine their relationship with K. pneumoniae population structure. Genomic analysis revealed three main lineages of K. pneumoniae, which corresponded to the previously defined KpI, KpII and KpIII lineages. All three lineages exhibited high genetic diversity. Further phylogenetic analysis revealed a sub-lineage of KpI to be a major cause of CA infections in Malawi. The sub-lineage included the clonally related ST14 and ST15 of K. pneumoniae which cause hospital acquired infection in multiple settings across the globe, A large pool of AMR genes, was identified in the genomes of the Malawian isolates, including multiple ESBL and qnr genes. Plasmid-encoded CTX-M-15 was the most common type of ESBL that was identified. In common with E. coli from Malawi, AMR was not restricted to a particular clade of K. pneumoniae. These findings suggest that dissemination of AMR in the K. pneumoniae population in Malawi was either due to a combination of horizontal gene transfer and clonal expansion, or horizontal gene transfer alone. In conclusion, the thesis has shown that ESBL production and fluoroquinolone resistance is rapidly spreading in Malawi across multiple E. coli and K. pneumoniae lineages that are causing increasing levels of infection. As cephalosporins and fluoroquinolones remain the last resort antimicrobial agents in this setting, urgent action is needed to curb the spread of Gram-negative AMR pathogens.

Background Urinary tract infections (UTIs) are common in women, and during pregnancy can cause significant morbidity. Growing and greatly varying antimicrobial resistance (AMR) of Enterobacteriaceae, responsible for most UTIs, necessitates regular local AMR surveillance. In obstetric population, where beta-lactams are the mainstay for treatment of severe UTIs, particular focus should be placed on beta-lactam resistance. This study aimed to evaluate AMR rates and frequency of extended spectrum beta-lactamase (ESBL) and carbapenemase genes in uropathogenic Enterobacteriaceae among reproductive-age women in St. Petersburg, Russia. Materials/methods Urine samples were collected from consecutive reproductive-age women, who attended the D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology from October 2017 to November 2019, and cultured according to routine procedures. Susceptibility to antibiotics and ESBL production was determined using the disc diffusion method according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. All urine samples and Enterobacteriaceae isolates were tested for ESBL and carbapenemase genes using real-time PCR. Results Enterobacteriaceae were detected in 91 (56 pregnant and 35 non-pregnant) of 119 (76%) included women. The vast majority of Enterobacteriaceae strains were susceptible to nitrofurantoin, fosfomycin and meropenem (99–100%). The frequency of strains susceptible to penicillins and cephalosporins ranged from 59% to 82%; 78% of strains were susceptible to ciprofloxacin. ESBL production was phenotypically detected in 15 (16%) Enterobacteriaceae strains, with CTX-M genes revealed in all cases. In all corresponding urine samples, CTX-M genes were also detected. The remaining 104 urine samples were negative for CTX-M genes. In none of the isolates and urine samples, carbapenemase genes were present. Conclusions The frequency of ESBL producing Enterobacteriaceae was relatively high (16%), with CTX-M genes detected in all cases in both urine and urine cultures. Rapid PCR detection of CTX-M genes directly in urine samples from women with pyelonephritis can be valuable for timely informing treatment choices.

Objectives: This study evaluated the diagnostic performance of the eazyplex® SuperBug CRE (eSBCRE) system, based on a loop-mediated isothermal amplification (LAMP), for the detection of the most common extended-spectrum beta-lactamases (ESBL) and carbapenemase genes in 140 clinical isolates of Escherichia coli. Materials and Methods: ESBL (blaCTX-M-1group and blaCTX-M-9group) and carbapenemase (blaKPC, blaVIM, blaNDM, blaOXA-48, and blaOXA-181) genes were detected using the eSBCRE test and compared with the results obtained by PCR, real-time PCR, and phenotypic methods. Results: Concordant results of 100% between PCR/real-time PCR and eSBCRE assays were observed. Two of 140 E. coli isolates were positive for both ESBL and carbapenemase genes according to eSBCRE, PCR, and real-time PCR assays, whereas they were negative in double-disk synergy test. Of 16 E. coli isolates suspected of producing carbapenemase, 9 were positive for 48-oxacillinases (OXA-48) by 30 μg temocillin test, whereas the blaOXA-48 was found only in 1 E. coli isolate by all molecular methods. Maximum threshold time values (minutes:seconds) in the eSBCRE test were 6:00, 11:15, 11:00, and 9:00 for the blaCTX-M-1group, blaCTX-M-9group, blaVIM, and blaOXA-48 genes, respectively. Conclusions: The eSBCRE test based on LAMP method is a reliable, easy-to-use, and timesaving molecular system, which can be successfully used in the routine diagnostic for the rapid detection of the most common ESBL and carbapenemase genes among clinical E. coli isolates.

Introduction: Urinary Tract Infections (UTIs) are a common yet serious medical condition that can impact individuals of all ages and genders. UTIs in Chronic Kidney Disease (CKD) patients lead to a low quality of life, and the situation becomes worse when the pathogens exhibit antibiotic resistance due to Extended Spectrum Beta-Lactamases (ESBLs), Metallo-BetaLactamases (MBLs), and Carbapenemase genes. Aim: To to evaluate the clinical profile, antibiotic resistance, and frequency of resistance genes in Klebsiella pneumoniae isolates from urine samples of suspected UTIs in CKD patients. Materials and Methods: This cross-sectional study was conducted at Yenepoya Medical College Hospital in Mangalore, Karnataka, India, from January 2023 to January 2024. A total of 138 Klebsiella spp. isolates were collected and included in the study. Antimicrobial susceptibility was assessed using the Vitek2 method. The production of MBL, carbapenemase, and ESBL was confirmed by tests described in the Clinical and Laboratory Standards Institute (CLSI) 2023 document, and genes were detected using multiplex Polymerase Chain Reaction (PCR). Statistical analyses were expressed as percentages for all quantitative data, and categorical variables were compared using Fisher’s exact test, with a p-value of <0.001 considered significant. Results: Among the study participants, 79 (57.25%) were male, and approximately 84 (60.87%) were over 50 years of age. About 46 (33.33%) patients had a history of recurrent UTIs and stage 1 renal impairment. A total of 85 (61.59%) of Klebsiella spp. isolates exhibited Multidrug Resistance (MDR). The maximum resistance was observed against ceftazidime and cefepime, while lower resistance was noted for amikacin, gentamicin, piperacillin-tazobactam, and trimethoprim-sulfamethoxazole. Eighteen of the MDR isolates (72%) carried β-lactamase genes, such as bla-SHV and bla-CTX-M. Additionally, 33 (82.5%) had bla-KPC, 21 (52.5%) had bla-IMP, and OXA genes (58, 23, 51, and 48) were found in 2 (2.8%) isolates each. Conclusion: The present study emphasises the significance of the co-occurrence of ESBL and carbapenemase-encoding genes in K. pneumoniae isolates implicated in UTIs among CKD patients, which could pose challenges for effective treatment options.

BackgroundMulti-drug resistance (MDR) and extensive-drug resistance (XDR) associated with extended-spectrum beta-lactamases (ESBLs) and carbapenemases in Gram-negative bacteria are global public health concerns. Data on circulating antimicrobial resistance (AMR) genes in Gram-negative bacteria and their correlation with MDR and ESBL phenotypes from Nepal is scarce.MethodsA retrospective study was performed investigating the distribution of ESBL and carbapenemase genes and their potential association with ESBL and MDR phenotypes in E. coli, Klebsiella spp., Enterobacter spp. and Acinetobacter spp. isolated in a major tertiary hospital in Kathmandu, Nepal, between 2012 and 2018.ResultsDuring this period, the hospital isolated 719 E. coli, 532 Klebsiella spp., 520 Enterobacter spp. and 382 Acinetobacter spp.; 1955/2153 (90.1%) of isolates were MDR and half (1080/2153) were ESBL producers. Upon PCR amplification, blaTEM (1281/1771; 72%), blaCTXM-1 (930/1771; 53%) and blaCTXM-8 (419/1771; 24%) were the most prevalent ESBL genes in the enteric bacilli. BlaOXA and blaOXA-51 were the most common blaOXA family genes in the enteric bacilli (918/1771; 25%) and Acinetobacter spp. (218/382; 57%) respectively. Sixteen percent (342/2153) of all isolates and 20% (357/1771) of enteric bacilli harboured blaNDM-1 and blaKPC carbapenemase genes respectively. Of enteric bacilli, Enterobacter spp. was the most frequently positive for blaKPC gene (201/337; 60%). The presence of each blaCTX-M and blaOXA were significantly associated with non-susceptibility to third generation cephalosporins (OR 14.7, p < 0.001 and OR 2.3, p < 0.05, respectively).The presence of each blaTEM, blaCTXM and blaOXA family genes were significantly associated with ESBL positivity (OR 2.96, p < 0.001; OR 14.2, p < 0.001 and OR 1.3, p < 0.05 respectively) and being MDR (OR 1.96, p < 0.001; OR 5.9, p < 0.001 and OR 2.3, p < 0.001 respectively).ConclusionsThis study documents an alarming level of AMR with high prevalence of MDR ESBL- and carbapenemase-positive ESKAPE microorganisms in our clinical setting. These data suggest a scenario where the clinical management of infected patients is increasingly difficult and requires the use of last-resort antimicrobials, which in turn is likely to intensify the magnitude of global AMR crisis.

Purpose: The purpose of this study was to detect biofilm formation in clinical isolates of Acinetobacter species and to observe correlation between biofilm formation and antimicrobial resistance among Acinetobacter isolates. Methods: Two hundred fifty six clinical samples collected from patients who were admitted in Intensive Care Unit (ICU) and on device, patients from Surgery, Medicine, Gynae &amp; Obs and Urology department of Bangabandhu Sheikh Mujib Medical University (BSMMU) and from Burn unit of Dhaka Medical College Hospital were included in this study. Biofilm formation and antibiotyping were performed for the isolates of Acinetobacter species recovered from clinical samples including tracheal aspirates, blood, urine, wound swab, pus, throat swab, endotracheal tubes, burn samples, ascitic fluid, sputum, aural swab, oral swab, cerebrospinal fluid, and catheter tip. Correlation of biofilm formation with antimicrobial resistance pattern among Acinetobacter isolates were also observed in this study. Result: A total of 256 various specimens were studied of which 95 Intensive Care Unit (ICU) and 161 Non ICU samples. Out of 95 ICU and 161 Non ICU samples, Acinetobacter species were isolated from 32 (33.7%) and 20(12.4%) respectively. From 32 ICU and 20 Non ICU Acinetobacter isolates, 28 (87.5%) and 11 (55%) were biofilm producers. Biofilm forming capacity of Acinetobacter species was significantly (p&lt;0.008) greater in ICU than in Non ICU isolates. In both ICU and Non ICU isolates, biofilm forming Acinetobacter species were 100% resistant to amoxicillin, ceftriaxone, ceftazidime, cefotaxime, cefuroxime, and aztreonam. Resistance to antibiotics such as gentamicin, amikacin, netilmicin, ciprofloxacin and imipenem was higher among biofilm forming Acinetobacter isolates in ICU than Non ICU isolates. Susceptibility to colistin was 100% in Non ICU isolates but in ICU it showed 7.1% resistance. Conclusions: This investigation showed that most of the clinical isolates of Acinetobacter species were biofilm producers especially from ICU samples and they were multidrug resistant. Even polymixin resistant Acinetobacter isolates are slowly emerging. This is very alerming for us that biofilm forming multidrug resistant Acinetobacter species represents a severe threat in the treatment of hospitalized patients. So, antibiotic policy and guidelines are essential to eliminate major outbreak in future.DOI: http://dx.doi.org/10.3329/jom.v14i1.14533 J MEDICINE 2013; 14 : 28-32

A modification of the needle-tubing combination for the push-pull machine used for aspiration-irrigation of congenital and traumatic cataracts, is described. The new needle-tubing-handle combination is advantageous in that the incorporated handle makes the insertion and maneouvring in the anterior chamber easier and also the whole combination can easily be autoclaved as silastic tubing is used.

BackgroundKlebsiella pneumoniae is a leading cause of bloodstream infection (BSI). Strains producing extended-spectrum beta-lactamases (ESBLs) or carbapenemases are considered global priority pathogens for which new treatment and prevention strategies are urgently required, due to severely limited therapeutic options. South and Southeast Asia are major hubs for antimicrobial-resistant (AMR) K. pneumoniae and also for the characteristically antimicrobial-sensitive, community-acquired “hypervirulent” strains. The emergence of hypervirulent AMR strains and lack of data on exopolysaccharide diversity pose a challenge for K. pneumoniae BSI control strategies worldwide.MethodsWe conducted a retrospective genomic epidemiology study of 365 BSI K. pneumoniae from seven major healthcare facilities across South and Southeast Asia, extracting clinically relevant information (AMR, virulence, K and O antigen loci) using Kleborate, a K. pneumoniae-specific genomic typing tool.ResultsK. pneumoniae BSI isolates were highly diverse, comprising 120 multi-locus sequence types (STs) and 63 K-loci. ESBL and carbapenemase gene frequencies were 47% and 17%, respectively. The aerobactin synthesis locus (iuc), associated with hypervirulence, was detected in 28% of isolates. Importantly, 7% of isolates harboured iuc plus ESBL and/or carbapenemase genes. The latter represent genotypic AMR-virulence convergence, which is generally considered a rare phenomenon but was particularly common among South Asian BSI (17%). Of greatest concern, we identified seven novel plasmids carrying both iuc and AMR genes, raising the prospect of co-transfer of these phenotypes among K. pneumoniae.ConclusionsK. pneumoniae BSI in South and Southeast Asia are caused by different STs from those predominating in other regions, and with higher frequency of acquired virulence determinants. K. pneumoniae carrying both iuc and AMR genes were also detected at higher rates than have been reported elsewhere. The study demonstrates how genomics-based surveillance—reporting full molecular profiles including STs, AMR, virulence and serotype locus information—can help standardise comparisons between sites and identify regional differences in pathogen populations.

BackgroundMultidrug resistance Enterobacteriaceae causing community-acquired pyelonephritis is an emerging threat; most isolates are EBSL, as per Indian data. After the results of the MERINO trial, most guidelines favors Carbapenem for treating community-acquired pyelonephritis. Overuse of carbapenem may lead to Carbapenem resistance Enterobacteriaceae (CRE) in the community. We analyzed the ESBL and CRE genes in the clinically significant urinary isolates with phenotypic ESBL -E from patients with community-acquired pyelonephritis.Table 1Demographic characteristics of patients with community-acquired acute pyelonephritis caused by phenotypic ESBL -E.MethodsPatients with a diagnosis of community-acquired acute pyelonephritis with age ≥ 18 years and urine culture showing the growth of Enterobacteriaceae with phenotypic ESBL-E are included in the study. If urine culture grew more than one organism in Enterobacteriaceae, other GNBs were excluded. The phenotypic ESBL detection was based on resistance to a third-generation cephalosporin (Cefotaxime, Cefpodoxime, Ceftazidime) and a monobactam (Aztreonam). These positive isolates were further processed using the combination disk method. A ≥5mm increase in zone diameter for either antimicrobial agent tested in combination with clavulanate vs the zone diameter of the agent when tested alone was considered ESBL (Clinical and Laboratory Standards Institute (CLSI) Performance standards for antimicrobial susceptibility tests). Simultaneously, multiplexed Real-time PCR (TRUPCR® UTI AST Panel Kit, Europe) was done to detect ESBL genes (CTX-M, TEM, SHV) and CRE genes (OXA-48, KPC, NDM, VIM, IMP) in these isolates.Table 2:Detection of NDM genes with ESBL genes in patients with community-acquired acute pyelonephritis caused by phenotypic ESBL -E.ResultsA total of 38 isolates with phenotypic ESBL in patients diagnosed with community-acquired pyelonephritis were processed for RT-PCR, and 30 were detected with ESBL and CRE genes. The demographic and clinical characteristics are shown in Table 1. The most common ESBL gene was CTX-M 29 (.96.7%) followed by TEM 25 (83.3%). Multiple ESBL genes were detected in 24(80%) isolates. Among CRE genes, the NDM genes were detected in 15 (50%) isolates with other ESBL genes (Table 2).ConclusionThe presence of CRE genes in phenotypic ESBL -E in community-acquired acute pyelonephritis could be due to the injudicious use of carbapenem. This may imply that CRE will be spread in the community in the future, making it difficult to manage this infection.DisclosuresAll Authors: No reported disclosures

ObjectivesNeonatal sepsis, a major cause of death amongst infants in sub-Saharan Africa, is often gut derived. Gut colonisation by Enterobacteriaceae producing extended spectrum beta-lactamase (ESBL) or carbapenemase enzymes can lead to antimicrobial-resistant (AMR) or untreatable infections. We sought to explore the rates of colonisation by ESBL or carbapenemase producers in two neonatal units (NNUs) in West and East Africa.MethodsStool and rectal swab samples were taken at multiple timepoints from newborns admitted to the NNUs at the University College Hospital, Ibadan, Nigeria and the Jaramogi Oginga Odinga Teaching and Referral Hospital, Kisumu, western Kenya. Samples were tested for ESBL and carbapenemase genes using a previously validated qPCR assay. Kaplan–Meier survival analysis was used to examine colonisation rates at both sites.ResultsIn total 119 stool and rectal swab samples were taken from 42 infants admitted to the two NNUs. Colonisation with ESBL (37 infants, 89%) was more common than with carbapenemase producers (26, 62.4%; P = 0.093). Median survival time before colonisation with ESBL organisms was 7 days and with carbapenemase producers 16 days (P = 0.035). The majority of ESBL genes detected belonged to the CTX-M-1 (36/38; 95%), and CTX-M-9 (2/36; 5%) groups, and the most prevalent carbapenemase was blaNDM (27/29, 93%).ConclusionsGut colonisation of neonates by AMR organisms was common and occurred rapidly in NNUs in Kenya and Nigeria. Active surveillance of colonisation will improve the understanding of AMR in these settings and guide infection control and antibiotic prescribing practice to improve clinical outcomes.

Antimicrobial resistance and resistance mechanisms of Enterobacteriaceae in ICU and non-ICU wards in Europe and North America: SMART 2011-2013.

Resistance to common antibiotics is a matter of grave concern in treating infections in hospital settings especially in Intensive Care Units (ICUs). One of the most commonly used and effective group of antibiotics, cephalosporins, exhibit resistance due to production of Extended Spectrum Beta- Lactamases (ESBLs). The prevalence of ESBL producing Escherichia coli (E.coli) has increased throughout the world and is a major cause of treatment failure in ICUs. As per our knowledge studies were not available on the prevalence of ESBL producing E.coli in ICUs of this region. To determine the prevalence of ESBLs among Escherichia coli isolates in ICUs of a tertiary care hospital. A cross sectional study was conducted over a period of 4 years (Sept 2011 to Sept 2015) in the Department of Microbiology, Kalinga Institute of Medical Sciences (KIMS), Bhubaneswar. Consecutive non-duplicate isolates of E.coli recovered from 6800 clinical samples of patients admitted to different Intensive Care Units (ICUs) were subjected to ESBL screening test and then to CLSI recommended Phenotypic Confirmatory Disc Diffusion Tests (PCDDT) for ESBL production determination. Out of 6800 samples, 1038 were E.coli isolates and 452(44%) were resistant to third generation cephalosporins. ESBL producing Escherichia coli among them were 276 (61.1%). Paediatric ICU showed the highest prevalence of ESBL E.coli at 80.9%. The highest prevalence of ESBL E.coli was in urine samples (82.6%) followed by pus (9.8%). The most effective antibiotic for ESBL producers was imipenem (96.7% sensitive), followed by amikacin (88.4%) and piperacillin- tazobactum (87%). This study has highlighted the high prevalence of ESBL producing E.coli in the ICUs of our hospital. An in depth analysis of their antibiogram will be helpful in formulating the antibiotic policy and prevent spread of ESBL strains. It is recommended that ESBL testing should be done routinely to curtail antibiotic resistance and to effectively implement infection control measures.

Distribution of extended-spectrum beta-lactamase genes using a commercial DNA micro-array system

We evaluated the changes in antibiotic resistance from 1998 to 2009 of Klebsiella pneumoniae isolated from the intensive care units (ICUs) and urology services of 14 Dutch hospitals and the consequences for empirical therapy. Quantitative antibiotic susceptibility testing of K. pneumoniae was performed in a central laboratory using a microbroth dilution method. Breakpoints were as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). The prevalence of extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing isolates was determined. A significant increase in resistance among ICU isolates was observed for ceftazidime (4.2%-10.8%), ciprofloxacin (5.8%-18.5%) and trimethoprim/sulfamethoxazole (11.9%-23.1%), and for cefuroxime (2.8%-7.9%) and trimethoprim/sulfamethoxazole (13.5%-27.8%) among urology isolates. Among ICU isolates the prevalence of ESBLs increased significantly from 2% to 8%. Carbapenemase production was not demonstrated. Among ICU isolates the prevalence of multidrug resistance increased and has been ≥12% since 2004. Among urology isolates multidrug resistance was highest in 2009 at 7.4%. Overall, resistance was significantly higher among ICU isolates. We observed an increase in resistance among ICU and urology isolates and an increased prevalence of ESBLs among ICU isolates. Carbapenemase production was not demonstrated. A regular update of empirical treatment protocols based on actual surveillance data is justified.

The rise of Multidrug-resistant (MDR) Enterobacter species is a significant global health concern, particularly in hospital settings where they contribute to nosocomial infections. This study aimed to determine the prevalence of MDR Enterobacter spp. in clinical specimens from Khartoum State, Sudan, to detect key resistance genes (CTX-M, AmpC, OXA-48, NDM-1, VIM, IMP, MCR-1, SHV, and TEM), and to analyze the correlation between genotypic and phenotypic resistance patterns. A cross-sectional, laboratory-based study was conducted from February to October 2021. A total of 384 clinical specimens, including urine, wound swabs, sputum, and blood, were collected from hospitals in Khartoum. Enterobacter spp. isolates were identified using conventional methods such as colony morphology, Gram staining, and biochemical tests. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method. Multiplex Polymerase Chain Reaction (PCR) was employed to detect ESBL genes (CTX-M, SHV, TEM, AmpC) and carbapenemase genes (OXA-48, NDM-1, VIM, IMP, MCR-1). Among the 384 clinical specimens, 14 (3.6%) were confirmed as Enterobacter spp. by PCR. All isolates exhibited multidrug resistance. CTX-M was detected in 100% of isolates, while SHV and TEM genes were absent. Other detected resistance genes included AmpC in 5 isolates (35.7%), IMP in 2 (14.3%), NDM-1 in 3 (21.4%), VIM in 5 (35.7%), OXA-48 in 7 (50.0%), and MCR-1 in 13 (92.9%). The predominance of CTX-M, car-bapenemase genes, and the absence of SHV and TEM suggest a distinct resistance profile in these isolates. The findings highlight a concerning emergence of MDR Enterobacter spp. in Sudan, primarily driven by the widespread presence of CTX-M and carbapenemase genes. The lack of SHV and TEM genes indicates potential regional differences in genetic resistance patterns. This underscores the critical need for molecular monitoring and effective infection control policies. The high prevalence of MDR Enterobacter spp., particularly due to CTX-M and carbapenemase gene expression, poses a serious threat to public health in Khartoum. Regional variation in resistance mechanisms, such as the absence of SHV and TEM, necessitates targeted antimicrobial stewardship and the development of localized treatment guidelines to limit the spread of resistance in Sudanese healthcare facilities.