Characterization of phenotypic and genotypic traits of carbapenem-resistant Acinetobacter baumannii clinical isolates recovered from a tertiary care hospital in Taif, Saudi Arabia

Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii with Special Reference to Carbapenemases: A Systematic Review

Carbapenemases are β-lactamase enzymes that hydrolyze a variety of β-lactams including carbapenem and belong to different Ambler classes (A, B, D). These enzymes can be encoded by plasmid or chromosomal-mediated genes. The major issues associated with carbapenemases-producing organisms are compromising the activity and increasing the resistance to carbapenems which are the last resort antibiotics used in treating serious infections. The global increase of pathogen, carbapenem-resistant A. baumannii has significantly threatened public health. Thus, there is a pressing need for a better understanding of this pathogen, to know the various carbapenem resistance encoding genes and dissemination of resistance genes from A. baumannii which help in developing strategies to overcome this problem. The horizontal transfer of resistant determinants through mobile genetic elements increases the incidence of multidrug, extensive drug, and Pan-drug resistant A. baumannii. Therefore, the current review aims to know the various mechanisms of carbapenem resistance, categorize and discuss carbapenemases encoding genes and various mobile genetic elements, and the prevalence of carbapenemase genes in recent years in A. baumannii from various geographical regions.

Extended Spectrum- and Carbapenemase-Based β-Lactam Resistance in the Arabian Peninsula-A Descriptive Review of Recent Years

Antimicrobial resistance (AMR) is a global problem that also includes countries of the Arabian Peninsula. Of particular concern, is the continuing development of extended-spectrum β-lactamases (ESBLs) in the countries of this region. Additionally, antibiotic treatment options for ESBL-producing bacteria are becoming limited, primarily due to the continuing development of carbapenem resistance (CR), carbapenems being frequently used to treat such infections. An overview of recent publications (2018-2021) indicates the presence of ESBL and/or CR in patients and hospitals in most countries of the Arabian Peninsula, although the delay between microbial isolation and publication inevitably makes an accurate analysis of the current situation rather difficult. However, there appears to be greater emphasis on CR (including combined ESBL and CR) in recent publications. Furthermore, although publications from Saudi Arabia are the most prevalent, this may simply reflect the increased interest in ESBL and CR within the country. Enhanced ESBL/CR surveillance is recommended for all countries in the Arabian Peninsula.

A rare occurrence of multidrug-resistant environmental Acinetobacter baumannii strains from the soil of Mangaluru, India

Over the last decade, Acinetobacter baumannii has emerged as one of the main causes of infections acquired in the hospital setting. Outbreaks associated with this pathogen are caused mainly due to contamination and transmission in hospital territories. However, the natural habitats of A. baumannii of clinical significance still remain unclear. In this study, we highlight the isolation and identification of multidrug-resistant environmental strains of A. baumannii from the soil of Mangaluru city. All the recovered isolates were biofilm formers, and two isolates were multidrug-resistant and showed resistance to fluoroquinolone, aminoglycosides, sulfonamide, tetracycline, and carbapenems. In addition, they exhibited protease activity, and produced phospholipase C and siderophore. To the best of our knowledge, this is the first study to isolate and identify drug-resistant strains of A. baumannii from the soil.

Clinical Distribution Characteristics of 1439 Carbapenem-Resistant Escherichia coli Strains in China: Drug Resistance, Geographical Distribution, Antibiotic MIC50/90

Purpose

To explore the clinical distribution characteristics and antimicrobial susceptibilities of carbapenem-resistant Escherichia coli (CR-ECO) in Hebei Province, China, from 2017 to 2019, and provide data on the treatment of this bacterial infection and the prevention of its spread.

Materials and Methods

A total of 1439 CR-ECO strains were collected from 2017 to 2019 in Hebei Province, China. Drug sensitivity tests were performed using the minimum inhibitory concentration (MIC) method, and the data were analyzed statistically using WHONET5.6 software.

Results

A total of 54,377 strains of Escherichia coli were isolated in Hebei Province from 2017 to 2019, of which 1439 strains were CR-ECO (2.65%). The highest proportion (33.78%) of strains was isolated from urine, and the detection rate showed a slow downward trend over the past 3 years. CR-ECO was mainly detected in densely populated and economically developed areas. Of all the patients, 54.2% were from the medical ward; the ratio of male to female patients with CR-ECO infections was 1.35:1; elderly patients and adults accounted for 59.6% and 30.8%, respectively, whereas minors and newborns accounted for 4.9% and 4.7%, respectively. For CR-ECO, the drug resistance rates to β-lactams were all higher than 80% and there was an annual increasing trend, while the drug resistance rates to quinolones remained nearly unchanged. The rate of resistance to aminoglycosides was relatively low, especially to amikacin (approximately 22%). The MIC50 of other antibacterial drugs, except amikacin, was equal to or higher than the break point of drug resistance.

Conclusion

From 2017 to 2019, the isolation rate of CR-ECO in Hebei Province, China, remained stable; however, the drug resistance rate showed an upward trend, primarily in cases of urinary tract infections in older men; the resistance rate to amikacin was the lowest.

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The First Saudi Study Investigating the Plasmid-borne Aminoglycoside and Sulfonamide Resistance among Acinetobacter baumannii Clinical Isolates Genotyped by RAPD-PCR: the Declaration of a Novel Allelic Variant Called aac(6')-SL and Three Novel Mutations in the sul1 Gene in the Acinetobacter Plasmid (s)

Background

Acinetobacter baumannii (A. baumannii) is one of the most important nosocomial pathogens responsible for a wide range of infections.

Aim

This study aimed to investigate the existence of the plasmidic genes encoding for aminoglycoside modifying enzymes (AMEs), 16S rRNA methyltransferases (RMT), and the altered dihydropetroate synthase (DHPS) encoded by the sul1 gene among A. baumannii clinical isolates collected from Taif, Kingdom of Saudi Arabia (KSA). The mutations in aac(6ʹ)-Ib and sul1 genes were also investigated.

Methods

Forty A. baumannii clinical isolates were investigated for their susceptibility to ten antibiotics. The plasmid DNA was extracted and screened for nine genes encoding for aminoglycoside resistance in addition to the sul1 gene. The clonal relatedness was determined by random amplified polymorphic DNA (RAPD)-PCR. Mutation in aac(6ʹ)-Ib and the sul1 genes were detected by capillary electrophoresis sequencing (CES).

Results

All isolates were A. baumannii in which 42.5% of them exhibited a high level of aminoglycoside resistance (HLAR). The most prevalent AMEs and RMT encoding genes were aph(3ʹ)-VI, the two aac(6ʹ) gene variants [aac(6ʹ)-Ib and aac(6ʹ)-SL], ant(3ʹʹ)-I, and armA in which 90%, 87.5%, 85%, and 45% of isolates tested positive, respectively. The other investigated aminoglycoside resistant encoding genes, namely aac(3)-II, aac(6ʹ)-II, and rmtB, were not detected. Only 15% of isolates harbored the sul1 gene. RAPD-PCR classified the 40 isolates into three clusters in which cluster II was the main cluster. DNA sequencing revealed that 34.29% (12/35) of isolates tested positive for aac(6ʹ)-Ib were found to harbor a common missense mutation in position 102 indicating a novel allelic variant named aac(6ʹ)-SL. Also, DNA sequencing revealed three missense mutations in the sul1 gene.

Conclusion

This is the first Saudi study to investigate the plasmid borne aminoglycoside and sulfonamide resistance genes among A. baumannii clinical isolates. A novel allelic variant for aac(6ʹ)-Ib was detected in addition to novel mutations in the sul1 gene.

Subtypes, resistance and virulence platforms in extended-drug resistant Acinetobacter baumannii Romanian isolates

Acinetobacter baumannii has emerged worldwide as a dominant pathogen in a broad range of severe infections, raising an acute need for efficient antibacterials. This is the first report on the resistome and virulome of 33 extended drug-resistant and carbapenem-resistant A. baumannii (XDR CRAB) strains isolated from hospitalized and ambulatory patients in Bucharest, Romania. A total of 33 isolates were collected and analyzed using phenotypic antibiotic susceptibility and conjugation assays, PCR, whole-genome sequencing (WGS), pulsed-field gel electrophoresis (PFGE) and MultiLocus Sequence Typing (MLST). All isolates were extensively drug-resistant (XDR), being susceptible only to colistin. The carbapenem resistance was attributed by PCR mainly to bla_OXA-24 and bla_OXA-23 genes. PFGE followed by MLST analysis demonstrated the presence of nine pulsotypes and six sequence types. WGS of seven XDR CRAB isolates from healthcare-associated infections demonstrated the high diversity of resistance genes repertoire, as well as of mobile genetic elements, carrying ARGs for aminoglycosides, sulphonamides and macrolides. Our data will facilitate the understanding of resistance, virulence and transmission features of XDR AB isolates from Romanian patients and might be able to contribute to the implementation of appropriate infection control measures and to develop new molecules with innovative mechanisms of action, able to fight effectively against these bugs, for limiting the spread and decreasing the infection rate and mortality.

Antimicrobial susceptibility of gram-positive and gram-negative bacteria: a 5-year retrospective analysis at a multi-hospital healthcare system in Saudi Arabia

BACKGROUND

Studying time-related changes in susceptible pathogens causing healthcare-associated infections (HAIs) is vital in improving local antimicrobial and infection control practices.

OBJECTIVES

Describe susceptibility patterns to several antimicrobials in gram-positive and gram-negative pathogens isolated from patients causing HAIs at three private tertiary care hospitals in Saudi Arabia over a 5-year period.

METHODS

Data on trends of antimicrobial susceptibility among bacteria causing HAIs events in children and adults at three tertiary private hospitals located in Riyadh and Qassim, Saudi Arabia, were collected retrospectively between 2015 and 2019 using the surveillance data datasets.

RESULTS

Over a 5-year period, 38,624 pathogens caused 17,539 HAI events in 17,566 patients. About 9450 (53.8%) of patients who suffered HAIs were females and the average age was 41.7 ± 14.3 years (78.1% were adults and 21.9% were children). Gram-negative pathogens were 2.3-times more likely to cause HAIs compared to gram-positive bacteria (71.9% vs. 28.1%). The ranking of causative pathogens in decreasing order was: Escherichia coli (38%), Klebsiella species (15.1%), and Staphylococcus aureus (12.6%). Gram-positive isolates were mostly susceptible to linezolid (91.8%) whereas they were resistant to ampicillin (52.6%), cefoxitin (54.2%), and doxycycline (55.9%). Gram-negative isolates were mostly sensitive to tigecycline (95%) whereas they were resistant to cefotaxime (49.5%) and cefixime (59.6%). During the 5 years, there were relatively stable susceptibility patterns to all tested antimicrobials, except for cefotaxime which shown a susceptibility reduction by 41.4%, among Escherichia coli and Klebsiella species. An increase in the susceptibility of Acinetobacter and Enterobacter and Citrobacter species to all studied antimicrobials was observed except for colistin that had a slight sensitivity reduction in 2019 by 4.3% against Acinetobacter species. However, we noted reduced sensitivity of MRSA, CoNS and Enterococcus species to gentamicin; and increased resistance of MRSA to linezolid and vancomycin.

CONCLUSION

The observed increase in susceptibility of gram-positive and gram-negative bacteria to studied antimicrobials is important; however, reduced sensitivity of MRSA, CoNS and Enterococcus species to gentamicin; and increased resistance of MRSA to linezolid and vancomycin is a serious threat and calls for effective antimicrobial stewardship programs.

Identification, Speciation and Antibiogram along with Detection of Metallo Beta-lactamase Production in Acinetobacter Isolated from Clinical Samples in a Tertiary Care Hospital

Acinetobacter species are gram negative non fermenters, which are important nosocomial pathogens involved in various outbreaks in hospitals due to widespread resistance to majority antibiotics. The aim of this study is to speciate Acinetobacter isolated from clinical samples, to assess the antibiotic sensitivity pattern and to detect the production of metallo-β-lactamase by double disc synergy test. The study was conducted in the department of microbiology, A. J Institute of Medical Sciences. All clinical samples were subjected to gram stain & cultured; the Acinetobacter isolates obtained were subjected to antibiogram. Those isolates that showed Imipenem resistant were further tested for production of metallo-β-lactamase by double disc synergy test. Out of 6625 culture positive isolates, 414 (36.1%) were identified biochemically to belong to Acinetobacter species. Of the 414 cases, 393 (94.9%) were further identified to be Acinetobacter baumannii and the remaining 21 (5.1%) to be Acinetobacter lwoffi. Acinetobacter lwoffii showed 100% sensitivity to all the drugs. Of the 393 Acinetobacter baumannii isolates 109 (27.7%) showed resistant to Imipenem. Out of these 109 isolates, 65 (59.63%) were positive for metallo-β-lactamase production by double disk synergy test. The speciation is highly demanding and laborious but it’s important to be demonstrated due to difference in the antibiotic susceptibility pattern. Carbapenem resistant Acinetobacter nosocomial strains in ICUs are detected to be more resistant to antibiotics. As shown in this study the metallo-β-lactamase producing A.baumannii isolates were 59.63% and therapeutic options were limited. Therefore early identification of metallo-β-lactamase producers is of great importance to start appropriate treatment and to control the spread.

Epidemiology, Susceptibility, and Risk Factors Associated with Mortality in Carbapenem-Resistant Gram-Negative Bacterial Infections Among Abdominal Solid Organ Transplant Recipients: A Retrospective Cohort Study

Introduction

Carbapenem-resistant gram-negative bacteria (CR-GNB) can cause life-threatening infections among abdominal solid organ transplantation (ASOT) recipients. This study aimed to investigate the epidemiology and drug susceptibility of CR-GNB pathogens and identity the risk factors associated with 90-day crude mortality of CR-GNB infections among ASOT recipients.

Methods

We retrospectively reviewed the clinical characteristics, drug resistance rate, and risk factors associated with mortality in CR-GNB infections among ASOT recipients between August 1, 2013, and August 1, 2020. The Cox regression model was performed to identify the independent risk factors for mortality.

Results

During the 8-year period, CR-GNB infections occurred in 153 of 1452 (10.5%) recipients, and 23 of 153 (15.0%) patients died. The most common pathogen was Acinetobacter baumannii (n = 47). The drug resistance rate of CR-GNB pathogens was relatively low to tigecycline (33.3%) and high to other categories (> 60%). There was a significant increasing trend in drug resistance to tigecycline as time went on (from 24 to 40%, P = 0.04). The independent risk factors for mortality were mechanical ventilation (hazard ratio 7.40, 95% confidence interval 2.69–20.38, P < 0.001), septic shock (hazard ratio 7.41, 95% confidence interval 2.86–19.23, P < 0.001), and platelet count < 50,000/mm³ (hazard ratio 4.00, 95% confidence interval 1.49–10.76, P = 0.006).

Conclusion

CR-GNB is widespread with high prevalence and mortality rates among ASOT recipients. Mechanical ventilation, septic shock, and low platelet count represent three independent risk factors related to the mortality of ASOT recipients with CR-GNB infection. We suggest that tigecycline may be used under rigorous management because of the significant increasing risk of drug resistance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40121-021-00411-z.

Cefoperazone/sulbactam: New composites against multiresistant gram negative bacteria?

Sulbactam, a class A β-lactamase inhibitor, added to cefoperazone either at a fixed 8 mg/L level of sulbactam or at a level of fixed cefoperazone: sulbactam ratio (2:1) would constitute a combination form of cefoperazone/sulbactam, which has better activities against Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii than cefoperazone alone. Cefoperazone/sulbactam (1:1 or 1:2) has greater in-vitro activity against most multidrug-resistant organisms (ESBL- and AmpC-producing Enterobacteriaceae and carbapenem-resistant A. baumannii except for carbapenem-resistant P. aeruginosa) than a 2:1 ratio. However, increased sulbactam concentration may induce AmpC production. Besides, sulbactam concentration might not be readily achievable in serum if the susceptibility rates were defined by the breakpoints of higher sulbactam composites, such as ≤16/16 (1:1) or 16/32 (1:2) mg/L. Carbapenemases (KPC-, OXA-type enzymes and metallo-β-lactamases) can't be inhibited by sulbactam. Some in-vitro studies showed that increasing sulbactam composites of cefoperazone/sulbactam had no effect on carbapenem-resistant P. aeruginosa, suggesting the presence of carbapenemases or AmpC overproduction that could not be overcome by increasing sulbactam levels to recover cefoperazone activity. Sulbactam alone has good intrinsic activity against carbapenem-resistant Acinetobacter strains sometimes even in the presence of carbapenemase genes, suggesting unsteady levels of carbapenemases. In conclusion, appropriate composites of cefoperazone and β-lactamase inhibitor sulbactam may expand the clinical use if the pharmacokinetic optimization could be achieved in the human serum.

Prevalence of OXA-Type β-Lactamase Genes among Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates in Thailand

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a critical health concern for the treatment of infectious diseases. The aim of this study was to investigate the molecular epidemiology of CRAB emphasizing the presence of oxacillinase (OXA)-type β-lactamase-encoding genes, one of the most important carbapenem resistance mechanisms. In this study, a total of 183 non-repetitive CRAB isolates collected from 11 tertiary care hospitals across Thailand were investigated. As a result, the blaoxa-51-like gene, an intrinsic enzyme marker, was detected in all clinical isolates. The blaoxa-23-like gene was presented in the majority of isolates (68.31%). In contrast, the prevalence rates of blaoxa-40/24-like and blaoxa-58-like gene occurrences in CRAB isolates were only 4.92% and 1.09%, respectively. All isolates were resistant to carbapenems, with 100% resistance to imipenem, followed by meropenem (98.91%) and doripenem (94.54%). Most isolates showed high resistance rates to ciprofloxacin (97.81%), ceftazidime (96.72%), gentamicin (91.26%), and amikacin (80.87%). Interestingly, colistin was found to be a potential drug of choice due to the high susceptibility of the tested isolates to this antimicrobial (87.98%). Most CRAB isolates in Thailand were of ST2 lineage, but some belonged to ST25, ST98, ST129, ST164, ST215, ST338, and ST745. Further studies to monitor the spread of carbapenem-resistant OXA-type β-lactamase genes from A. baumannii in hospital settings are warranted.

Biofilm-Formation in Clonally Unrelated Multidrug-Resistant Acinetobacter baumannii Isolates

This study analyzed the genotype, antibiotic resistance, and biofilm formation of Acinetobacter baumannii strains and assessed the correlation between biofilm formation, antibiotic resistance, and biofilm-related risk factors. A total of 207 non-replicate multi-drug-resistant A. baumannii strains were prospectively isolated. Phenotypic identification and antimicrobial susceptibility testing were carried out. Isolate biofilm formation ability was evaluated using the tissue culture plate (TCP), Congo red agar, and tube methods. Clonal relatedness between the strains was assessed by enterobacterial repetitive intergenic consensus-PCR genotyping. Of the 207 isolates, 52.5% originated from an intensive care unit setting, and pan resistance was observed against ceftazidime and cefepime, with elevated resistance (99–94%) to piperacillin/tazobactam, imipenem, levofloxacin, and ciprofloxacin. alongside high susceptibility to tigecycline (97.8%). The Tissue culture plate, Tube method, and Congo red agar methods revealed that 53.6%, 20.8%, and 2.7% of the strains were strong biofilm producers, respectively, while a significant correlation was observed between biofilm formation and device-originating respiratory isolates (p = 0.0009) and between biofilm formation in colonized vs. true infection isolates (p = 0.0001). No correlation was detected between antibiotic resistance and biofilm formation capacity, and the majority of isolates were clonally unrelated. These findings highlight the urgent need for implementing strict infection control measures in clinical settings.

Carbapenemases: Transforming Acinetobacter baumannii into a Yet More Dangerous Menace

Acinetobacter baumannii is a common cause of serious nosocomial infections. Although community-acquired infections are observed, the vast majority occur in people with preexisting comorbidities. A. baumannii emerged as a problematic pathogen in the 1980s when an increase in virulence, difficulty in treatment due to drug resistance, and opportunities for infection turned it into one of the most important threats to human health. Some of the clinical manifestations of A. baumannii nosocomial infection are pneumonia; bloodstream infections; lower respiratory tract, urinary tract, and wound infections; burn infections; skin and soft tissue infections (including necrotizing fasciitis); meningitis; osteomyelitis; and endocarditis. A. baumannii has an extraordinary genetic plasticity that results in a high capacity to acquire antimicrobial resistance traits. In particular, acquisition of resistance to carbapenems, which are among the antimicrobials of last resort for treatment of multidrug infections, is increasing among A. baumannii strains compounding the problem of nosocomial infections caused by this pathogen. It is not uncommon to find multidrug-resistant (MDR, resistance to at least three classes of antimicrobials), extensively drug-resistant (XDR, MDR plus resistance to carbapenems), and pan-drug-resistant (PDR, XDR plus resistance to polymyxins) nosocomial isolates that are hard to treat with the currently available drugs. In this article we review the acquired resistance to carbapenems by A. baumannii. We describe the enzymes within the OXA, NDM, VIM, IMP, and KPC groups of carbapenemases and the coding genes found in A. baumannii clinical isolates.

The First Egyptian Report Showing the Co-Existence of bla NDM-25, bla OXA-23, bla OXA-181, and bla GES-1 Among Carbapenem-Resistant K. pneumoniae Clinical Isolates Genotyped by BOX-PCR

Background and Objective

The emergence of carbapenem-resistant K. pneumoniae (CRKP) continues to escalate and is alarming because of the emergence of pan drug-resistant strains. The objective of this study was to investigate the existence of 12 carbapenemase genes among CRKP clinical isolates.

Methods

Ninety-six Klebsiella spp. clinical isolates were collected. The isolates were identified phenotypically and genotypically. These isolates were screened for susceptibility to 24 different antibiotics. The modified Hodge test (MHT) and the Carba Nordmann/Poirel (NP) test were used to phenotypically screen carbapenem-resistant strains for carbapenemase production. Phenotypic characterization of carbapenemases was performed using the combined disk synergy test (CDST). Additionally, the presence of 12 carbapenemase genes in CRKP isolates was investigated. The DNA sequence of bla _NDM and bla _GES genes was determined. The BOX-PCR technique was used to determine the clonal relationship between CRKP isolates.

Results

All carbapenem-resistant isolates were related to K. pneumoniae. Susceptibility testing showed that 19.79% (19/96) of the collected isolates were carbapenem-resistant. Of the CRKP isolates, 68.42% (13/19) tested positive for the MHT and Carba NP test. CDST showed that 42.11% (8/19), 63.16% (12/19), 47.37% (9/19), and 73.68% (14/19) of the CRKP isolates tested positive for the inhibitory effect of clavulanic acid, sulbactam, phenylboronic acid, and tazobactam, respectively, while 84.21% (16/19) and 68.42% (13/16) tested positive for the inhibitory effect of EDTA and mercaptopropionic acid, respectively. It was found that 10.53% (2/19) of the isolates tested positive for the inhibitory effect of sodium chloride. Molecular investigation of carbapenemases showed that 26.32% (5/19), 73.68% (14/19), 21.05% (4/19), 10.53% (2/19), and 5.26% (1/19) of the isolates tested positive for bla _NDM, bla _OXA-48, bla _OXA-181, bla _OXA-51, and bla _OXA-23, respectively. None of the isolates tested positive for bla _OXA-40 and bla _OXA-58. Two allelic variants of bla _NDM (bla _NDM-1 and bla _NDM-25) were detected. BOX-PCR revealed high clonal relatedness between CRKP isolates.

Conclusion

MHT was more sensitive than Carba NP test for evaluating carbapenemase production and class D carbapenemase genes were the most prevalent of the 12 carbapenemase genes that were evaluated.