Distribution of CTX-M group I and group III β-lactamases produced by Escherichia coli and klebsiella pneumoniae in Lahore, Pakistan

Frequency of Fecal Carriage of ESBL Resistance Genes in Multidrug-Resistant Pseudomonas aeruginosa Isolates from Cancer Patients at Laquintinie Hospital, Douala, Littoral Region, Cameroon

Background. Opportunistic infections are the second cause of death among cancer patients. This study aimed at determining the antimicrobial profile and the prevalence of extended-spectrum beta-lactamase (ESBL)-gene carriage of Pseudomonas aeruginosa isolates among cancer patients at the Douala Laquintinie Hospital, Littoral Region of Cameroon. Between October 2021 and March 2023, 507 study participants were recruited among whom 307 (60.55%) were cancer patients, compared to 200 (39.45%) noncancer patients. Fifty-eight P. aeruginosa isolates were isolated from fecal samples of forty-five cancer patients and thirteen noncancer patients using Cetrimide agar. The antimicrobial resistance profile of the isolates was determined using the Kirby-Bauer disk diffusion method. The polymerase chain reaction was used to detect the presence of extended-spectrum beta-lactamase genes among P. aeruginosa isolates. P. aeruginosa showed significant resistance rates in cancer patients compared to noncancer patients to imipenem, cefotaxime, and ceftazidime, piperacillin-tazobactam, ticarcillin-clavulanic acid, and ciprofloxacin. The multidrug resistance (MDR) rate was significantly (p < 0.05) higher in cancer patients than in noncancer patients. The frequency of beta-lactamase genes in the 58 ESBL-producing P. aeruginosa isolates was determined as 72.41% for bla TEM, 37.93% for bla OXA, 74.14% for blaCTX-M, and 44.83% for bla SHV genes. The study revealed an alarmingly high prevalence of fecal carriage of ESBL-producing P. aeruginosa with a high rate of MDR among cancer patients. It indicates that regular monitoring and surveillance of ESBL-producing P. aeruginosa among cancer patients are needed to improve the management of patients.

The Rising Tide of Antibiotic Resistance: A Study on Extended-Spectrum Beta-Lactamase and Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae

BACKGROUND

The global spread of extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant Enterobacterales (CRE) poses a significant concern. Acquisition of antimicrobial resistance genes leads to resistance against several antibiotics, limiting treatment options. We aimed to study ESBL-producing and CRE transmission in clinical settings.

METHODS

From clinical samples, 227 ESBL-producing and CRE isolates were obtained. The isolates were cultured on bacterial media and confirmed by VITEK 2. Antibiograms were tested against several antibiotics using VITEK 2. The acquired resistance genes were identified by PCR.

RESULTS

Of the 227 clinical isolates, 145 (63.8%) were Klebsiella pneumoniae and 82 (36.1%) were Escherichia coli; 76 (33.4%) isolates were detected in urine, 57 (25.1%) in pus swabs, and 53 (23.3%) in blood samples. A total of 58 (70.7%) ESBL-producing E. coli were resistant to beta-lactams, except for carbapenems, and 17.2% were amikacin-resistant; 29.2% of E. coli isolates were resistant to carbapenems. A total of 106 (73.1%) ESBL-producing K. pneumoniae were resistant to all beta-lactams, except for carbapenems, and 66.9% to ciprofloxacin; 38 (26.2%) K. pneumoniae were resistant to carbapenems. Colistin emerged as the most effective antibiotic against both bacterial types. Twelve (20.6%) E. coli isolates were positive for blaCTX-M, 11 (18.9%) for blaTEM, and 8 (33.3%) for blaNDM. Forty-six (52.3%) K. pneumoniae isolates had blaCTX-M, 27 (18.6%) blaTEM, and 26 (68.4%) blaNDM.

CONCLUSION

This study found a high prevalence of drug-resistant ESBL-producing and CRE, highlighting the need for targeted antibiotic use to combat resistance.

A systematic review and meta-analysis of carbapenem resistance and its possible treatment options with focus on clinical Enterobacteriaceae: Thirty years of development in Pakistan

Background

Carbapenem resistance is epidemic worldwide, these last resort antimicrobials are listed in the WHO 'watch group' with higher resistance potential. During the years 2017-18 Pakistan Antimicrobial Resistance Surveillance System reported an increase in carbapenem resistance. However, a comprehensive information on prevalence and molecular epidemiology of carbapenem resistance in Pakistan is not available. This systematic review and meta-analysis is aimed to report the current carbapenem resistance situation in Pakistan and its treatment options.

Methods

In this systematic review and meta-analysis, we investigated the pooled prevalence (PPr) of carbapenem resistance in Enterobacteriaceae and non-Enterobacteriaceae by organizing available data, from Web of Science and PubMed by April 2, 2020, in various groups and subgroups including species, years, provinces, extended spectrum β-lactamase production, clinical presentation, carbapenemase and metallo-β-lactamase production, and New Delhi metallo-β-lactamase (NDM) prevalence. Literature review was updated for the studies publisehd by December 07, 2023. Moreover, we descriptively reviewed the molecular epidemiology of carbapenem resistance in Enterobacteriaceae and non-Enterobacteriaceae in Pakistan. Lastly, we statistically explored different treatment options available for carbapenem resistant infections. We used R package 'metafor' for performing meta-analysis and influence diagnostics and determining treatment options.

Results

From two academic databases Web of Science and PubMed we identified 343 studies. Eighty-eight studies were selected for the systematic review and meta-analysis. Seventy-four studies were selected for phenotypic analysis, 36 for genotypic analysis, and 31 for available treatment options. PPr-ID of 12% [0.12 (0.07, 0.16)] was observed for phenotypic carbapenem resistance in Enterobacteriaceae with more prevalence recorded in Klebsiella pneumoniae 24% [0.24 (0.05, 0.44)] followed by 9% [0.09 (-0.03, 0.20)] in Escherichia coli. During the last two decades we observed a striking increase in carbapenem resistance PPr i.e., from 0% [0.00 (-0.02, 0.03)] to 36% [0.36 (0.17, 0.56)]. blaNDM with PPr 15% [0.15 (0.06, 0.23)] in naive isolates was found to be the fundamental genetic determinant for carbapenem resistance in Enterobacteriaceae in Pakistan. Polymyxin B, colistin, tigecycline, and fosfomycin were identified as the suggested treatment options available for multidrug resistant infections not responding to carbapenems. Various studies reported carbapenem resistance from human, animal, and environment sources.

Conclusion

In conclusion, we found that NDM-1 producing carbapenem resistant Enterobacteriaceae are increasing in Pakistan. Meta-analysis showed that metallo-β-lactamases producing E. coli ST405 and K. pneumoniae sequence type11 are the major resistant clones. Number of reported studies in various subgroups and inconsistency in following CLSI guidelines are the potential limitations of this meta-analysis. A National antimicrobial resistance (AMR) surveillance strategy based on One Health is urgently needed to check any future AMR crisis in Pakistan.

Extended-Spectrum β-Lactamases (ESBL): Challenges and Opportunities

The rise of antimicrobial resistance, particularly from extended-spectrum β-lactamase producing Enterobacteriaceae (ESBL-E), poses a significant global health challenge as it frequently causes the failure of empirical antibiotic therapy, leading to morbidity and mortality. The E. coli- and K. pneumoniae-derived CTX-M genotype is one of the major types of ESBL. Mobile genetic elements (MGEs) are involved in spreading ESBL genes among the bacterial population. Due to the rapidly evolving nature of ESBL-E, there is a lack of specific standard examination methods. Carbapenem has been considered the drug of first choice against ESBL-E. However, carbapenem-sparing strategies and alternative treatment options are needed due to the emergence of carbapenem resistance. In South Asian countries, the irrational use of antibiotics might have played a significant role in aggravating the problem of ESBL-induced AMR. Superbugs showing resistance to last-resort antibiotics carbapenem and colistin have been reported in South Asian regions, indicating a future bleak picture if no urgent action is taken. To counteract the crisis, we need rapid diagnostic tools along with efficient treatment options. Detailed studies on ESBL and the implementation of the One Health approach including systematic surveillance across the public and animal health sectors are strongly recommended. This review provides an overview of the background, associated risk factors, transmission, and therapy of ESBL with a focus on the current situation and future threat in the developing countries of the South Asian region and beyond.

Antibacterial efficacy of silver nanoparticles (AgNPs) against metallo-β-lactamase and extended spectrum β-lactamase producing clinically procured isolates of Pseudomonas aeruginosa

Resistance to carbapenems is a global threat, especially in developing countries with limited health resources. Prevalence, antibiogram, PCR detection of antibiotic resistance genes, and potency of Silver Nanoparticles (AgNPs) against multidrug-resistant (MDR) Pseudomonas aeruginosa were studied. Kirby-Bauer disc method and PCR were used to study antibiogram and drug resistance genes respectively in 255 isolates of Pseudomonas aeruginosa obtained from a tertiary care hospital. Silver nitrate (AgNO₃) precursor salts were reacted with Aspergillus flavus culture filtrate to trigger the extracellular mycosynthesis of AgNPs. Mycosynthesis was first monitored regularly by visible ultraviolet spectroscopy that recorded AgNP peaks of approximately 400-470 nm. Confirmation by Transmission electron micrographs provided confirmation of AgNPs formed within a range of 5-30 nm. Individual and combined antibacterial activity of ten antibiotics and AgNPs was analyzed. Pearson correlation coefficients (r) were calculated for phenotypic and genotypic multidrug resistance. Data were evaluated using SPSS version 20. p-value < 0.05 was considered statistically significant. 61.5% were carbapenemase producers (p < 0.01). The recorded frequency of bla_IMP-1, bla_SHV, bla_VIM, bla_OXA, and bla_TEM were 13%, 32%, 15%, 21%, and 43%, respectively. The reducing order of antimicrobial activity of antibiotics and AgNPs was piperacillin/tazobactam + AgNPs (31 mm), cefoxitin + AgNPs (30 mm) > amikacin + AgNPs (25 mm) > aztreonam + AgNPs (23 mm) > meropenem + AgNPs (22 mm) > imipenem + AgNPs (20 mm) > gentamycin + AgNPs (17 mm) > ciprofloxacin + AgNPs (16 mm) > cefoperazone/sulbactam + AgNPs (14 mm) ≥ ceftazidime + AgNPs (14 mm). The conjugated effect of AgNPs plus antibiotics showed a 0.15-3.51 (average of 2.09) fold-area augmentation of antimicrobial activity. AgNPs conjugated with antibiotics effectively inhibited MDR Pseudomonas aeruginosa. To the best of our understanding, this is an inaugural report from Punjab Pakistan enlisting co-expression of Metallo-β-lactamases, extended-spectrum β-lactamases, and AmpC-β-lactamase plus activity of antibiotic-AgNPs.

Molecular characterization of Enterobacter aerogenes isolated from urinary tract infections in Iran

The prevalence of multidrug-resistant Enterobacter aerogenes strains in UTIs is increasing. Therefore, the purpose of this study was to examine the mechanisms of resistance in Enterobacter aerogenes strains isolated from the urinary tract of infected patients. To achieve this goal, 786 urine samples from Shahrekord, Iran, were collected from June 2019 to February 2020. After isolating and identifying E. aerogenes samples, antibiotic susceptibility testing was done on the strains using Kirby-Bauer's disk diffusion method. The biofilm formation assays were performed to study the link between antibiotic resistance and biofilm formation and virulence genes. As a result, amongst the 786 urine samples, 50 strains were identified as E. aerogenes. The lowest rate of resistance was observed with imipenem (30%). This study also reports that all the strains of E. aerogenes are biofilm producers, with 50% of isolates producing a large amount, 30% a moderate amount, and 20% a small amount of biofilm. 42% were identified in the phenotypic study of ESBLs. In the PCR test, (64%) produced broad-spectrum beta-lactamases. Prevalence of qnrC, qnrB, qnrA, tetA, tet B, acc(3)IIa, acc(2)IIa, ant(2)Ia and Sul1 in strong producing isolates reported 100%, 80.95%,% 58.14, 87.5%, 81.58%, 86.67%, 82.14, 81.48% and 90% respectively. In the statistical analysis based on the chi-square test, a statistically significant relationship was reported between qnrA, qnrB, tetA, tetB, Sul1, ant(2)Ia, ant(3)I, aac(3)II, and biofilm formation. Resistance to cephalothin, ceftriaxone, cefotaxime and ceftazidime were reported 40%, 34%, 30% and 30%, respectively. Out of 50 Enterobacter aerogenes, 32 isolates (64%) were identified in the phenotypic study of ESBLS, prevalence of bla_CTX-M, bla_TEM and bla_SHV reported 30%, 20% and 14% respectively. There is a significant relationship between resistance to ceftriaxone and bla_CTX-M. Prevalence of csgA, ybtS, markD, rmpA, csgD and fimH in strong biofilm formation isolates reported 84%, 83.33%, 80%, 80%, 80% and 66% respectively. The chi-square test showed a statistically significant relationship between biofilm production and resistance genes fimH, csgA, csgD, ybtS, and mrkD. The findings of this study indicate that the ability to produce biofilms is associated with the increase of antibiotic resistance and virulence genes. These agents enable bacteria to produce biofilms that ultimately lead to colonization and bacterial survival in the body.

Conventional and Real-Time PCR Targeting blaOXA Genes as Reliable Methods for a Rapid Detection of Carbapenem-Resistant Acinetobacter baumannii Clinical Strains

Multidrug-resistant Acinetobacter baumannii, particularly those producing carbapenemases, are spread worldwide. A reliable detection of carbapenemases is essential to choose the appropriate antimicrobial therapy and, consequently, prevent the dissemination of carbapenem-resistant strains. The aim of this study is to examine the molecular basis of the carbapenem resistance mechanism and estimation of conventional PCR and real-time PCR usefulness for the detection of oxacillinases when compared to phenotypic carbapenemases detection. The following methods were evaluated: the CarbAcineto NP test, Carbapenem Inactivation Method, CPO panels of semiautomated antimicrobial susceptibility testing method on the BD Phoenix™ M50 system, conventional Polymerase Chain Reaction and real-time PCR. The eazyplex^® SuperBug complete A assay was used as the reference method. Among the tested strains, 39 (67.2%) carried the bla_OXA-40 gene, while the bla_OXA-23 gene was noted amongst 19 (32.8%) isolates. The diagnostic sensitivities of the studied assays were as follows: CarbAcineto NP—65.5%; CIM—100%; CPO—100%; conventional PCR—100%; real-time PCR—100%.

The Evaluation of Eazyplex® SuperBug CRE Assay Usefulness for the Detection of ESBLs and Carbapenemases Genes Directly from Urine Samples and Positive Blood Cultures

Increasing antimicrobial resistance of Gram-negative rods is an important diagnostic, clinical and epidemiological problem of modern medicine. Therefore, it is important to detect multi-drug resistant strains as early on as possible. This study aimed to evaluate Eazyplex^® SuperBug CRE assay usefulness for beta-lactamase gene detection among Gram-negative rods, directly from urine samples and positive blood cultures. The Eazyplex^® SuperBug CRE assay is based on a loop-mediated isothermal amplification of genetic material and allows for the detection of a selection of genes encoding carbapenemases, KPC, NDM, VIM, OXA-48, OXA-181 and extended-spectrum beta-lactamases from the CTX-M-1 and CTX-M-9 groups. A total of 120 clinical specimens were included in the study. The test gave valid results for 58 (96.7%) urine samples and 57 (95.0%) positive blood cultures. ESBL and/or carbapenemase enzymes genes were detected in 56 (93.3%) urine and 55 (91.7%) blood samples, respectively. The Eazyplex^® SuperBug CRE assay can be used for a rapid detection of the genes encoding the most important resistance mechanisms to beta-lactams in Gram-negative rods also without the necessity of bacterial culture.

Molecular epidemiology of antibiotic-resistant genes and potent inhibitors against TEM, CTX-M-14, CTX-M-15, and SHV-1 proteins of Escherichia coli in district Peshawar, Pakistan

The Extended Spectrum Beta-Lactamases (ESBLs) producing bacteria is an issue of concern for clinicians resulting in minimize the treatment options. To overcome resistance mechanisms, novel inhibitors with good Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties must inhibit the ESBLs resistant genes. The current study aimed to identify the antibiotic resistance genes of ESBLs producing E. coli and a single inhibitor was designed to inhibit all the resistant proteins. The results showed that 42.9% ESBL producers had CTX-M (69.9%), TEM (63.4%), SHV (34.5%) and CTX-M-14 (17.5%) genes. The ESBLs producing isolates were resistant to cephalosporins, quinolones, and sulfonamide with Minimum Inhibitory Concentration (MICs) ranging from 64 to >256 μg/ml. To design multi inhibitory ligands, RECAP synthesis was used for the de-novo discovery of 1000 inhibitors database. Protein crystal structures were retrieved from Protein Data Base (PDB). Lipinski's rules of five were applied to the novel inhibitors database to improve the ADMET properties. The novel inhibitors database was selected for docking simulations. Placement of the ligand was used by the London dG algorithm implemented in Molecular Operating Environment (MOE), while GBVI/WSA dG algorithm was used for final refinement. Based on docking score, visual inspection of ligands interaction with key residues, binding affinity, and binding energy of ligands with proteins, ten compounds were selected for ESBLs proteins with best ADMET properties, binding energy, and binding affinity the reported ones. These hits compounds have unique scaffolds and are predicted to be a starting point for developing potent inhibitors against antibiotic-resistant proteins.

Molecular Epidemiology of mcr-1, bla KPC-2, and bla NDM-1 Harboring Clinically Isolated Escherichia coli from Pakistan

Purpose

The multiple-drug resistant Escherichia coli are among the deadliest pathogens causing life-threatening infections. This study was planned to determine the molecular epidemiology of mcr-1, bla _KPC-2, and bla _NDM-1 harboring clinically isolated E. coli from Pakistan.

Methods

In total, 545 strains of E. coli from clinical samples were collected from June 2018 to September 2019. All the isolates were screened for colistin-resistance, extended-spectrum-β-lactamases (ESBL), and carbapenemases through the micro-dilution method, Double-Disk-Synergy-Test (DDST), and Modified-Hodge-Test (MHT). The detection, sequence-typing, conjugal transfer, S1-PFGE, plasmid-replicon-typing, and southern-blotting for mcr, ESBL, and carbapenemase-encoding genes were performed.

Findings

A total of four (0.73%) colistin-resistant strains carrying alongside mcr-1 and bla _CTX-M-15 genes, three of these strains also had the bla _TEM-1 gene. The presence of ESBL genes was detected in 139 (25.5%) isolates harboring bla _CTXM-15 (74.82%), bla _TEM (34.53%), bla _SHV (28.06%) and bla _OXA-1 (28.78%). In 129 carbapenemase-producers, 35.83% possessed bla _NDM-1, 26.67% bla _KPC-2, 8.3% bla _OXA-48, 25% bla _VIM-1, and 20.83% bla _IMP-1 genes. The sequence typing revealed that mcr-1 harboring isolates belonged to ST405, ST117, and ST156. Fifty percent of bla _KPC-2 and 48.83% of bla _NDM-1 were found on ST131 and ST1196, respectively. Two rare types of STs, ST7584, and ST8671 were also identified in this study. The mcr-1 gene was located on Incl2 (60-kb) plasmid. The bla _KPC-2 was present on (140-kb) IncH12, (100-kb) IncN, (90-kb) Incl1, while bla _NDM-1 was located on (70-kb) IncFIIK, (140-kb) IncH12, (100-kb) IncN, (60-kb) IncA/C, and (45-kb) IncFII plasmids, which were successfully trans-conjugated. Among the plasmid types, the Incl1 carrying bla _KPC-2, IncH12 harboring bla _KPC-2 and bla _NDM-1, and IncFIIK carrying bla _NDM-1 were for the first time detected in Pakistan.

Conclusion

The mcr-1, bla _KPC-2, and bla _NDM-1 genes finding in various clonal and plasmids types indicate that a substantial selection of the resistance genes had occurred in our clinical strains.

Antibiotic resistance in Pakistan: a systematic review of past decade

Background

During the last six decades, extensive use of antibiotics has selected resistant strains, increasing the rate of fatal infectious diseases, and exerting an economic burden on society. This situation is widely accepted as a global problem, yet its degree is not well elucidated in many regions of the world. Up till now, no systemic analysis of Antimicrobial resistance (AMR) in Pakistan has been published. The current study aims to describe the antibiotic-resistance scenario of Pakistan from human samples of the last 10 y, to find the gaps in surveillances and methodology and recommendations for researchers and prescribers founded on these outcomes.

Methods

Original research articles analyzed the pattern of Antibiotic resistance of any World Health Organization (WHO) enlisted priority pathogens in Pakistan (published onward 2009 till March 2020), were collected from PubMed, Google scholar, and PakMedi Net search engines. These articles were selected based on predefined inclusion and exclusion criteria. Data about the study characteristics and antibiotic-resistance for a given bacterium were excluded from literature. Antibiotic resistance to a particular bacterium was calculated as a median resistance with 95% Confidence Interval (CI).

Results

Studies published in the last 10 y showed that Urinary Tract Infection (UTI) is the most reported clinical diagnosis (16.1%) in Pakistan. E. coli were reported in 28 (30.11%) studies showing high resistance to antibiotics’ first line. Methicillin-resistant Staphylococcus aureus (MRSA) was found in 49% of S. aureus’ total reported cases. Phenotypic resistance pattern has mostly been evaluated by Disk Diffusion Method (DDM) (82.8%), taken Clinical Laboratory Standards Institute (CLSI) as a breakpoint reference guideline (in 79.6% studies). Only 28 (30.11%) studies have made molecular identification of the resistance gene. blaTEM (78.94% in Shigella spp) and blaNDM-1 (32.75% in Klebsiella spp) are the prominent reported resistant genes followed by VanA (45.53% in Enterococcus spp), mcr-1 (1.61% in Acinetobacter spp), and blaKPC-2 (31.67% in E. coli). Most of the studies were from Sindh (40.86%), followed by Punjab (35.48%), while Baluchistan’s AMR data was not available.

Conclusion

Outcomes of our study emphasize that most of the pathogens show high resistance to commonly used antibiotics; also, we find gaps in surveillances and breaches in methodological data. Based on these findings, we recommend the regularization of surveillance practice and precise actions to combat the region’s AMR.

Distribution of NDM1 Carbapenemase-Producing Proteeae Strains on High-Risk Hospital Wards

Background

Carbapenem-resistant Proteeae (CRP) is a group of multidrug-resistant (MDR) microorganisms that raise special treatment problems due to their intrinsic resistance to colistin. In this study, our aim is to provide a phenotypic and molecular characterization of the carbapenemases secreted by CRP strains isolated from inpatients from an intensive care unit (ICU) and surgical wards, as well as the identification of the risk factors involved in their acquisition.

Methods

An observational, cross-sectional study was performed which included all Proteeae strains isolated in samples from inpatients on high-risk wards of the largest university hospital in Western Romania, from July 2017 to April 2019. Meropenem-resistant strains (N=65) with MIC ≥16 µg/mL were subjected to a singleplex PCR assay for the detection of blaNDM, blaVIM and blaCTX-M genes. The analysis of risk factors was performed by logistic regression.

Results

Out of 8317 samples that were processed, 400 Proteeae strains were isolated: 64% belonging to the genus Proteus, 26.75% to the genus Providencia and 9.25% to the genus Morganella. Most CRP strains (N=56) were of MBL type, and 55 had the blaNDM gene as the prevalent gene substrate. P. stuartii was the main species that provided the circulating MDR strains. Most CRP strains came from patients admitted to ICU, being isolated mainly from bronchial aspirates and blood cultures. Multivariate analysis revealed 3 independent risk factors – mechanical ventilation>96h (HR: 40.51 [13.65–120.25], p <0.001), tracheostomy (HR: 2.65 [1.14–6.17], p = 0.024) and prolonged antibiotic therapy (HR: 1.01 [1.00–1.02], p = 0.03).

Conclusion

There is a significant increase in the incidence of CR P. stuartii strains, the MBL-blaNDM type being predominant. These strains presented various other resistance mechanisms, being often extremely difficult to treat and led to an excess of lethality of 27.16%.

High frequency of simultaneous presence of ESBL and carbapenemase producers among nosocomial coliform isolates in Faisalabad, Pakistan

Objectives:

The objective of the current study was to find prevalence of relevant ESBL and carbapenemase producing genes in nosocomial E. coli and K. pneumoniae isolates and to check phenotypic susceptibility of all ESBL positive isolates to carbapenems.

Methods:

Forty ESBL producing clinical isolates of Escherichia coli (n=33) and Klebsiella pneumoniae (n=7) were examined for the presence of β-lactamase genes (CTX-M, CTX-M-1, 2, 3, 4 and TEM). Carbapenem resistance was checked phenotypically and by presence of blaNDM-1 gene.

Results:

Nine (27%) were positive for CTX-M genes, and 10 (30%) for TEM among E. coli isolates. Importantly, six isolates showed co-existence of CTX-M and TEM genes. In K. pneumoniae, two (28%) isolates were positive for CTX-M and one (14%) for TEM genes. Eight (24%) E. coli and one (14%) K. pneumoniae isolates were positive for CTX-M-1. Respective figures for CTX-M-4 were three (10%) and one (14%). CTX-M-2 and CTX-M-3 groups were not represented. Twenty (50%) isolates were resistant to both imipenem and meropenem out of which only four isolates expressed blaNDM-1 gene.

Conclusions:

The significant presence of both ESBL and carbapenemase producers and co-existence of ESBL and carbapenemases in the same isolates is worrisome.

Continuous rise in cephalosporin and fluoroquinolone consumption in Pakistan: a 5 year analysis (2014-18)

Background

Pakistan was third on the list of the highest antibiotic-consuming countries among low- and middle-income countries in 2015. Studies have suggested that areas with higher consumption of antibiotics are likely to have higher antibiotic resistance rates.

Objectives

With limited surveillance data on consumption and resistance in Pakistan, this study investigated the 5 year trends (April 2014 to March 2019) in consumption of the two highest-sold antibiotic classes, cephalosporins [Anatomical Therapeutic Chemical (ATC) group J01D] and fluoroquinolones (ATC group J01MA).

Methods

IQVIA Pakistan data (retail) on antibiotic sales presented in units were used. These data were standardized and a DDD was assigned to all formulations, based on WHO’s ATC/DDD index, and the data expressed as DIDs (DDDs per 1000 inhabitants per day). WHO’s AWaRe classification of antimicrobials was used for the analyses, especially of those categorized as ‘Watch’.

Results

The findings showed a significant increase in consumption trends for ‘Watch’ cephalosporins (61.5%) while the use of ‘Reserve’ cephalosporins doubled during the studied period. In 2018, combined consumption of second- and third-generation cephalosporins (both in the ‘Watch’ group) was nearly five times higher than that of the first-generation cephalosporins. For fluoroquinolones, the total consumption only showed a major increase for ciprofloxacin, with 127 820 more persons per day. The consumption of cephalosporins and fluoroquinolones in Pakistan increased by 1.86 DIDs in just 5 years.

Conclusions

It is urgent to establish a National Antimicrobial Commission in Pakistan, to critically analyse the pharmaceutical market offerings and implement surveillance systems and antimicrobial stewardship.

Distribution of bla CTX - M , bla TEM , bla SHV and bla OXA genes in Extended-spectrum-β-lactamase-producing Clinical isolates: A three-year multi-center study from Lahore, Pakistan

Background

Frequency of extended-spectrum-β-lactamase-producing clinical isolates is increasing worldwide. This is a multi-center study which was aimed to check the frequency of third-generation cephalosporin resistance and distribution of the key genetic determinants of Extended-spectrum-β-lactamase-producing Clinical isolates in Pakistan.

Methods

A total of 2372 samples were processed in three tertiary care hospitals and one diagnostic research center of Lahore, Pakistan during Aug-2014 to Sep-2017. Analytical profile index (API 20-E) was used for biochemical characterization of isolates. Antibiotic susceptibility testing (AST) and third generation cephalosporin resistant (3GC-R) isolates were subjected to: double disc synergism test (DDST), combination disc test (CDST) and epsilometric test (E-test) for confirmation of ESBL-production. PCR amplification of isolates with plasmid and genomic DNA was performed. Amplicon sequences were checked for gene-variants and statistical analyses were performed to check the significance of data.

Results

A total of 497/995 (50%) isolates including Escherichia coli 65% (n = 321), Klebsiella spp. 25% (n = 124) and Pseudomonas. 5% (n = 24), Enterobacter spp. 4% (n = 20) and Acinetobacter spp. 2% (n = 8) were screened as third generation cephalosporin resistant (3GC-R). Urine 56% (n = 278) followed by pus 20% (n = 99) and wound swab 6% (n = 29) were frequent sources. Incidence of ESBL-producers detected by combination disc test was 79% (n = 392). PCR revealed bla_{CTX − M} (76%) gene followed by bla_OXA (52%), bla_TEM (28%) and bla_SHV (21%) were most prevalent among ESBL-producers detected by CDST. bla_{CTX − M − 1}(65%), bla_OXA (78%) and bla_TEM (57%) genes were carried on plasmids. Amplicon sequencing revealed bla_{CTX − M − 15} (75%), bla_OXA − 1 (49%) and bla_{TEM − 1B} (34%) and 21 (n = 28) isolates carried three genes in them.

Conclusion

Prevalence of ESBL-producing isolates has increased 1.13 folds during study years. Isolates had high prevalence of ESBL-encoding bla_{CTXM − 15} gene and narrow spectrum bla_OXA − 1 and bla_{TEM − 1B} were also prevalent.

Serogroup distribution, diversity of exotoxin gene profiles, and phylogenetic grouping of CTX-M-1- producing uropathogenic Escherichia coli

The emergence of CTX-M-1 producing Uropathogenic Escherichia coli (UPEC) has become a serious challenge. In addition to antimicrobial resistance, a number of virulence factors have been shown. Therefore, this study was designed to determine the prevalence of O- serogroups, phylogenetic groups, exotoxin genes, and antimicrobial resistance properties of CTX-M-1- producing UPEC. A total of 248 UPEC isolates were collected. The antibiotic resistance was performed, and PCR was used to detect the bla_CTX-M1, exotoxins, serogroups and phylogroups of UPEC. Of 248 isolates, 95 (38.3%) harbored bla_CTX-M-1. Of them, serogroups O1 and O25 were predominant, accounting for 20% and 13.7%, respectively. The hlyA was the dominant exotoxin gene (32.6%), followed by sat (28.4%), vat (22.1%), cnf (13.7%), picU (8.4%), and cdt (2.1%). The hlyA gene was significantly associated with pyelonephritis (P =  0.003). Moreover, almost half of the isolates (45.4%) belonged to phylogenetic group B2. Most of exotoxin genes were present in significantly higher proportions in group B2 isolates except cdt gene (P <  0.05). All of the isolates were susceptible to imipenem, nitrofurantoin, and fosfomycin. The CTX-M-1-producing UPEC strains causing nosocomial infections are more likely to harbor certain exotoxin genes, raising the possibility that this increase in virulence genes may result in an increased risk of complicated UTI.

High frequency and molecular epidemiology of metallo-β-lactamase-producing gram-negative bacilli in a tertiary care hospital in Lahore, Pakistan

Background

Metallo-β-lactamase (MBL)-producing isolates have a strong impact on diagnostic and therapeutic decisions. A high frequency of MBL-producing gram-negative bacilli has been reported worldwide. The current study was based on determining the incidence of MBL-producing imipenem-resistant clinical isolates and investigating the β-lactamase gene variants in strains conferring resistance to a carbapenem drug (imipenem).

Methods

A total of 924 gram negative isolates were recovered from a tertiary care hospital in Lahore, Pakistan, during a two-year period (July 2015 to February 2017). The initial selection of bacterial isolates was based on antibiotic susceptibility testing. Strains resistant to imipenem were processed for the molecular screening of β-lactamase genes. Statistical analysis for risk factor determination was based on age, gender, clinical specimen and type of infection.

Results

The rate of imipenem resistance was calculated to be 56.51%. Among the 142 strains processed, the phenotypic tests revealed that the incidence of MBLs was 63.38% and 86.61% based on the combination disc test and the modified Hodge test, respectively. The frequencies of bla_TEM, bla_SHV,bla_OXA,bla_IMP-1, and bla_VIM genes were calculated to be 46%, 34%, 24%, 12.5% and 7%, respectively. The co-expression of bla_MBL (bla_IMP and bla_VIM) and bla_ESBL (bla_TEM, bla_SHV,bla_OXA) was also detected through multiplex and singleplex PCR. bla_OXA, bla_TEM and bla_SHV coexisted in 82% of the isolates. Co-expression of ESBL and MBL genes was found in 7% of the isolates.

Conclusion

To our knowledge, this is the first report from Pakistan presenting the concomitant expression of bla_OXA, bla_TEM and bla_SHV with bla_IMP-1 and bla_VIM in MBL-producing gram-negative bacilli.

Phenotypic and Molecular Characterization of Multidrug Resistant Klebsiella pneumoniae Isolated from Different Clinical Sources in Al-Najaf Province-Iraq

BACKGROUND AND OBJECTIVE

Burns infections and urinary tract infections are the most important prevalent diseases in Asian countries, such as Iraq. Klebsiella pneumoniae is one of the most important bacteria cause this type of infections especially in hospitals. Therefore, the aim of this study was to investigate the prevalence of multi-drug resistance K. pneumoniae and extended-spectrum beta-lactamases producing K. pneumoniae isolates from inpatients with urinary tract infection and burns infections in Al-Kufa hospital in Al-Najaf province, Iraq.

MATERIALS AND METHODS

A total of 285 clinical samples were collected from in-patients infected with urinary tract infection (141 urine samples) and burns infections (144 burns swabs). Fourteen different antibiotics were used by disc diffusion method and 13 antimicrobials resistance genes were used by PCR technique.

RESULTS

A total of 43 K. pneumoniae strains were isolated. The highest resistance rate was observed for amoxicillin 25 μg and amoxicillin+clavulanic acid 20+10 μg (97.67%) while the lowest resistance rate was observed for imipenem 10 μg (9.30%). The most common resistance associated-genes were blaSHV (86.04%) and at lower prevalence were IMP (9.30%).

CONCLUSION

Klebsiella pneumoniae strains isolated from burns infections were more virulent than those isolated from urinary tract infections.