Distribution of 16S rRNA methylases among different species of Gram-negative bacilli with high-level resistance to aminoglycosides

Molecular Typing of Multidrug-Resistant Acinetobacter baumannii Isolates from Clinical Specimens by ERIC-PCR and MLVA

Acinetobacter baumannii, a Gram-negative and oxidase-negative bacterium, is a major cause of nosocomial infections, leading to high mortality rates in hospitalized patients. The use of 2 prominent molecular typing methods (i.e., enterobacterial repetitive intergenic consensus-polymerase chain reaction [ERIC-PCR] and multiple-locus variable-number tandem repeat [VNTR] analysis [MLVA]) for genotyping A. baumannii isolates has proven to be an effective approach in assessing the clonal relation of these isolates and managing their outbreaks. A total of 100 A. baumannii isolates were collected from immunocompromised patients hospitalized in the intensive care unit (ICU) of a hospital in Zanjan City, Iran. Their antibiotic resistance ability (especially aminoglycoside resistance) was studied by disc diffusion tests. The genetic typing of A. baumannii was studied using ERIC-PCR and MLVA methods. All isolates were resistant to 3 or more antibiotics and regarded as multidrug-resistant (MDR). Additionally, 32% of the isolates were resistant to all antibiotics tested, and 91% were extensively drug-resistant (XDR). The increased rate of aminoglycoside-resistant A. baumannii in ICU patients, with an increased incidence of aminoglycoside-modifying enzymes of aac (6')-Ib, ant (3″)-I, and aph (2″)-Id. ERIC-PCR has likewise shown an increased level of diversity in A. baumannii isolates. According to the ERIC-PCR patterns, isolates were classified as 4 clusters, while according to the MLVA patterns, isolates were classified as 9 distinct clusters. ERIC-PCR and MLVA assays serve as useful genotyping methods to assess the genetic variety or clonal relatedness of A. baumannii isolates.

Exploring multidrug-resistant Klebsiella pneumoniae antimicrobial resistance mechanisms through whole genome sequencing analysis

BACKGROUND

Antibiotic-resistant Klebsiella pneumoniae has emerged as a critical public health threat worldwide. Understanding the antimicrobial resistance mechanisms of multidrug-resistant K. pneumoniae (MDR-Kp) and its prevalence in time and space would provide clinical significance for managing pathogen infection.

METHODS

Eighteen clinical MDR-Kp strains were analyzed by whole genome sequencing (WGS), and the antimicrobial resistance genes and associated resistance mechanisms were compared with results obtained from the conventional microbiological test (CMT). The sequence homology across strains in our study and those previously collected over time from a wide geographical region was assessed by phylogenetic analysis.

RESULTS

MDR-Kp strains were collected from eighteen patients who had received empirical treatment before strain collection, with sputum (83.3%, 15/18) being the primary source of clinical samples. The commonly received treatments include β-lactamase inhibitors (55.6%, 10/18) and carbapenems (50%, 9/18). Using CMT, we found that all 18 strains were resistant to aztreonam and ciprofloxacin, while 14 (77.8%) showed resistance to carbapenem. Polymyxin B and tigecycline were the only antibiotics to which MDR-Kp strains were sensitive. A total of 42 antimicrobial resistance mechanisms were identified by WGS, surpassing the 40 detected by the conventional method, with 25 mechanisms shared between the two techniques. Despite a 100% accuracy rate of WGS in detecting penicillin-resistant strains, the accuracy in detecting cephalosporin-resistant strains was only at 60%. Among all resistance genes identified by WGS, Klebsiella pneumoniae carbapenemase-2 (KPC-2) was present in all 14 carbapenem-resistant strains. Phenotypic analysis indicated that sequence type (ST) 11 isolates were the primary cause of these MDR-Kp infections. Additionally, phylogenic clustering analysis, encompassing both the clinical and MDR-Kp strains previously reported in China, revealed four distinct subgroups. No significant difference was observed in the sequence homology between K. pneumoniae strains in our study and those previously collected in East China over time.

CONCLUSION

The application of WGS in identifying potential antimicrobial-resistant genes of MDR-Kp has demonstrated promising clinical significance. Comprehensive genomic information revealed by WGS holds the promise of guiding treatment decisions, enabling surveillance, and serving as a crucial asset in understanding antibiotic resistance.

The Behavior of Some Bacterial Strains Isolated from Fallow Deer Compared to Antimicrobial Substances in Western Romania

(1) Background: The resistance levels of Escherichia coli, Salmonella spp., Pseudomonas spp., Staphylococcus spp., etc., isolated from the nasal cavity and the rectum of Dama dama deer from three hunting grounds in Western Romania were assessed. (2) Methods: The analysis was completed using the diffusimetric method, compliant with CLSI reference standards, and with Vitek-2 (BioMérieux, France), on 240 samples. (3) Results: The results were statistically analyzed (by one-way ANOVA) revealing that in four of the ten E. coli strains isolated from animals, 87.5% (p < 0.001) resistance was found. E. coli strains were resistant to cephalexin (100%); seven strains were resistant to cephalothin and ampicillin; six were resistant to cefquinome and cefoperazone; five were resistant to amoxicillin/clavulanic acid; and four were resistant to ceftiofur. However, E. coli was sensitive to amikacin (100%). The most efficient structures were beta-lactams, amikacin, and imipenem, to which all 47 strains studied (100%) were sensitive, followed by nitrofurantoin, to which 45 strains (95.7%) were sensitive, neomycin, to which 44 strains (93.6%) were sensitive, ceftiofur, to which 43 strains (91.5%) were sensitive, and trimethoprim/sulfamethoxazole and marbofloxacin, to which 42 strains (89.4%) were sensitive. (4) Conclusions: In wild animal populations, where a human presence is frequently reported, including a constant presence of domestic animals, despite the perceived low risk of emerging resistance to antimicrobials, resistance is likely to develop frequently.

Molecular epidemiology and transmission of rmtB-positive Escherichia coli among ducks and environment

This study aimed to investigate the transmission and molecular epidemiological characteristics of the rmtB gene in Escherichia coli (E. coli) strains isolated from duck farms in Guangdong Province of China from 2018 to 2021. A total of 164 (19.4%, 164/844) rmtB-positive E. coli strains were recovered from feces, viscera, and environment. We performed antibiotic susceptibility tests, pulsed-field gel electrophoresis (PFGE), and conjugation experiments. We obtained the genetic context of 46 rmtB-carrying E. coli isolates and constructed a phylogenetic tree via whole genome sequencing (WGS) and bioinformatic analysis. The isolation rate of rmtB-carrying E. coli isolates in duck farms increased yearly from 2018 to 2020 but decreased in 2021. All rmtB-harboring E. coli strains were multidrug resistant (MDR), and 99.4% of the strains were resistant to more than 10 drugs. Surprisingly, duck- and environment-associated strains similarly showed high MDR. Conjugation experiments revealed that the rmtB gene horizontally cocarried bla_CTX-M and bla_TEM gene dissemination via IncFII plasmids. Insertion sequences IS26, ISCR1, and ISCR3 were closely associated with the spread of rmtB-harboring E. coli isolates. WGS analysis indicated that ST48 was the most prevalent sequence type. The results of single nucleotide polymorphism (SNP) differences revealed potential clonal transmission between ducks and the environment. Based on One Health principles, we need to strictly use veterinary antibiotics, monitor the distribution of MDR strains, and evaluate the impact of plasmid-mediated rmtB gene on human, animal, and environmental health.

Occurrence of antibiotics and bacterial resistance genes in wastewater: resistance mechanisms and antimicrobial resistance control approaches

Antimicrobial pharmaceuticals are classified as emergent micropollutants of concern, implying that even at low concentrations, long-term exposure to the environment can have significant eco-toxicological effects. There is a lack of a standardized regulatory framework governing the permissible antibiotic content for monitoring environmental water quality standards. Therefore, indiscriminate discharge of antimicrobials at potentially active concentrations into urban wastewater treatment facilities is rampant. Antimicrobials may exert selective pressure on bacteria, leading to resistance development and eventual health consequences. The emergence of clinically important multiple antibiotic-resistant bacteria in untreated hospital effluents and wastewater treatment plants (WWTPs) has been linked to the continuous exposure of bacteria to antimicrobials. The levels of environmental exposure to antibiotics and their correlation to the evolution and spread of resistant bacteria need to be elucidated to help in the formulation of mitigation measures. This review explores frequently detected antimicrobials in wastewater and gives a comprehensive coverage of bacterial resistance mechanisms to different antibiotic classes through the expression of a wide variety of antibiotic resistance genes either inherent and/or exchanged among bacteria or acquired from the reservoir of antibiotic resistance genes (ARGs) in wastewater systems. To complement the removal of antibiotics and ARGs from WWTPs, upscaling the implementation of prospective interventions such as vaccines, phage therapy, and natural compounds as alternatives to widespread antibiotic use provides a multifaceted approach to minimize the spread of antimicrobial resistance.

Detection and characterisation of 16S rRNA methyltransferase-producing Pseudomonas aeruginosa from the UK and Republic of Ireland from 2003-2015

16S rRNA methyltransferase (16S RMTase) genes confer high-level aminoglycoside resistance, reducing treatment options for multidrug-resistant Gram-negative bacteria. Pseudomonas aeruginosa isolates (n = 221) exhibiting high-level pan-aminoglycoside resistance (amikacin, gentamicin and tobramycin MICs ≥64, ≥32 and ≥32 mg/L, respectively) were screened for 16S RMTase genes to determine their occurrence among isolates submitted to a national reference laboratory from December 2003 to December 2015. 16S RMTase genes were identified using two multiplex PCRs, and whole-genome sequencing (WGS) was used to identify other antibiotic resistance genes, sequence types (STs) and the genetic environment of 16S RMTase genes. 16S RMTase genes were found in 8.6% (19/221) of isolates, with rmtB4 (47.4%; 9/19) being most common, followed by rmtD3 (21.1%; 4/19), rmtF2 (15.8%; 3/19) and single isolates harbouring rmtB1, rmtC and rmtD1. Carbapenemase genes were found in 89.5% (17/19) of 16S RMTase-positive isolates, with bla_VIM (52.9%; 9/17) being most common. 16S RMTase genes were found in 'high-risk' clones known to harbour carbapenemase genes (ST233, ST277, ST357, ST654 and ST773). Analysis of the genetic environment of 16S RMTase genes identified that IS6100 was genetically linked to rmtB1; IS91 to rmtB4, rmtC or rmtD3; ISCR14 to rmtD1; and rmtF2 was linked to Tn3, IS91 or Tn1721. Although 16S RMTase genes explained only 8.6% of pan-aminoglycoside resistance in the P. aeruginosa isolates studied, the association of 16S RMTase genes with carbapenemase-producers and 'high-risk' clones highlights that continued surveillance is required to monitor spread as well as the importance of suppressing the emergence of dually-resistant clones in hospital settings.

Overcoming the rising incidence and evolving mechanisms of antibiotic resistance by novel drug delivery approaches - An overview

Antimicrobial resistance is a normal evolutionary process for microorganisms. Antibiotics exerted accelerated selective pressure that hasten bacterial resistance through mutation, and acquisition external genes. These genes often carry multiple antibiotic resistant determinants allowing the recipient microbe an instant "super-bug" status. The extent of Antimicrobial Resistance (AMR) has reached a level of global crisis, existing antimicrobials are no long effective in treating infections caused by AMR pathogens. The great majority of clinically available antimicrobial agents are administered through oral and intra-venous routes. Overcoming antibacterial resistance by novel drug delivery approach offered new hopes, particularly in the treatment of AMR pathogens in sites less assessible through systemic circulation such as the lung and skin. In the current review, we will revisit the mechanism and incidence of important AMR pathogens. Finally, we will discuss novel drug delivery approaches including novel local antibiotic delivery systems, hybrid antibiotics, and nanoparticle-based antibiotic delivery systems.

Heteroresistance to Amikacin in Carbapenem-Resistant Klebsiella pneumoniae Strains

Heteroresistance can lead to treatment failure and is difficult to detect by the methods currently employed by clinical laboratories. The aim of this study was to investigate the prevalence of the amikacin-heteroresistant Klebsiella pneumoniae strains and explore potential amikacin heteroresistance mechanism through whole-genome sequencing (WGS) and quantitative reverse-transcription PCR (qRT-PCR). In this study, 13 isolates (8.39%) were considered as amikacin-heteroresistant K. pneumoniae strains among a total of 155 K. pneumoniae strains. The majority of the heterogeneous phenotypes (11/13, 84.61%) was unstable and the minimal inhibitory concentrations (MICs) fully or partially reverted back to the level of susceptibility of the parental isolate. The frequency of heteroresistant subpopulation ranged from 2.94×10^-7 to 5.59×10^-6. Whole-genome sequencing and single-nucleotide variants (SNVs) analysis showed that there were different nucleotide and resultant amino acid alterations among an amikacin-heteroresistant strain S38 and the resistant subpopulation S38L in several genes. Quantitative reverse-transcription PCR analysis revealed that the increased expression of aminoglycoside resistance genes detected in amikacin-heteroresistant K. pneumoniae strains might be associated with amikacin heteroresistance. The findings raise concerns for the emergence of amikacin-heteroresistant K. pneumoniae strains and the use of amikacin as therapy for the treatment of multidrug-resistant K. pneumoniae strains.

A prospective surveillance study to determine the prevalence of 16S rRNA methyltransferase-producing Gram-negative bacteria in the UK

OBJECTIVES

To determine the prevalence of 16S rRNA methyltransferase- (16S RMTase-) producing Gram-negative bacteria in patients in the UK and to identify potential risk factors for their acquisition.

METHODS

A 6 month prospective surveillance study was conducted from 1 May to 31 October 2016, wherein 14 hospital laboratories submitted Acinetobacter baumannii, Enterobacterales and Pseudomonas aeruginosa isolates that displayed high-level amikacin resistance according to their testing methods, e.g. no zone of inhibition with amikacin discs. Isolates were linked to patient travel history, medical care abroad, and previous antibiotic exposure using a surveillance questionnaire. In the reference laboratory, isolates confirmed to grow on Mueller-Hinton agar supplemented with 256 mg/L amikacin were screened by PCR for 16S RMTase genes armA, rmtA-rmtH and npmA, and carbapenemase genes (blaKPC, blaNDM, blaOXA-48-like and blaVIM). STs and total antibiotic resistance gene complement were determined via WGS. Prevalence was determined using denominators for each bacterial species provided by participating hospital laboratories.

RESULTS

Eighty-four isolates (44.7%), among 188 submitted isolates, exhibited high-level amikacin resistance (MIC >256 mg/L), and 79 (94.0%) of these harboured 16S RMTase genes. armA (54.4%, 43/79) was the most common, followed by rmtB (17.7%, 14/79), rmtF (13.9%, 11/79), rmtC (12.7%, 10/79) and armA + rmtF (1.3%, 1/79). The overall period prevalence of 16S RMTase-producing Gram-negative bacteria was 0.1% (79/71 063). Potential risk factors identified through multivariate statistical analysis included being male and polymyxin use.

CONCLUSIONS

The UK prevalence of 16S RMTase-producing Gram-negative bacteria is low, but continued surveillance is needed to monitor their spread and inform intervention strategies.

Present and Future Perspectives on Therapeutic Options for Carbapenemase-Producing Enterobacterales Infections

Carbapenem-resistant Enterobacterales (CRE) are included in the list of the most threatening antibiotic resistance microorganisms, being responsible for often insurmountable therapeutic issues, especially in hospitalized patients and immunocompromised individuals and patients in intensive care units. The enzymatic resistance to carbapenems is encoded by different β-lactamases belonging to A, B or D Ambler class. Besides compromising the activity of last-resort antibiotics, CRE have spread from the clinical to the environmental sectors, in all geographic regions. The purpose of this review is to present present and future perspectives on CRE-associated infections treatment.

Prevalence of Aminoglycoside Resistance Genes and Molecular Characterization of a Novel Gene, aac(3)-IIg, among Clinical Isolates of the Enterobacter cloacae Complex from a Chinese Teaching Hospital

Members of the Enterobacter cloacae complex are important opportunistic human pathogens capable of causing a wide variety of infections. During recent decades, aminoglycoside-resistant E. cloacae complex isolates have increasingly been reported and have become a major concern. Here, we employed high-throughput sequencing in combination with specific PCR assays to investigate the prevalence of aminoglycoside resistance genes among 170 isolates of the E. cloacae complex collected from a teaching hospital in Wenzhou, China. A total of 12 known genes [aphA-1, strA, strB, aac(6')-IIc, aadA2, aac(3)-IId, aadB, aadA1, rmtB, armA, aadA5, and aac(6')-Ie-aph(2'')-Ia] and 1 novel gene [aac(3)-IIg] were identified, with aphA-1 (71.18%), strA (55.29%), and strB (52.35%) being the most prevalent, and aac(3)-IIg was detected with a positive rate of 21.76% (37/170). The aac(3)-IIg gene was 810 bp in length and encoded a protein that shared 72 to 78% identities with previously known AAC(3)-II aminoglycoside 3-N-acetyltransferases. The MICs of gentamicin and tobramycin were 512 μg/ml and 64 μg/ml, respectively, when aac(3)-IIg was cloned into Escherichia coli DH5α. All aac(3)-IIg-positive isolates exerted broad aminoglycoside resistance profiles, mediated by the coexistence of multiple resistance genes. Moreover, aminoglycoside resistance and resistance genes were found to be transferable in most strains (24/37). Nevertheless, pulsed-field gel electrophoresis (PFGE) and dendrogram analysis showed clonal diversity among these isolates. S1 nuclease PFGE, Southern hybridization, and whole-genome sequencing indicated that aac(3)-IIg was located on transferable as well as nontransferable plasmids of various sizes. The analysis of the genetic environment suggested that aac(3)-IIg is embedded within a class 1 integron, with IS26 playing an important role in its mobility.

Tentative epidemiologic cut-off value and resistant characteristic detection of apramycin against Escherichia coli from chickens

Escherichia coli are important foodborne zoonotic pathogens. Apramycin is a key aminoglycoside antibiotic used by veterinarians against E. coli. This study was conducted to establish the epidemiological cut-off value (ECV) and resistant characteristics of apramycin against E. coli. In this study, 1412 clinical isolates of E. coli from chickens in China were characterized. Minimum inhibitory concentrations (MICs) of apramycin were assessed by broth microdilution method. MIC50 and MIC90 for apramycin against E. coli (0.5-256 µg/mL) were 8 and 16 µg/mL, respectively. In this study, the tentative ECV was determined to be 16 µg/mL by the statistical method and 32 µg/mL by ECOFFinder software. Besides, the percentages of aac(3)-IV positive strains ascended with the increase of MIC values of apramycin, and the gene npmA was detected in strains with higher MICs. Sixteen apramycin highly resistant strains displayed multiple drug resistance (100%) to amoxicillin, ampicillin, gentamicin, doxycycline, tetracycline, trimethoprim and florfenicol, while most of them were susceptible to amikacin and spectinomycin. In summary, the tentative ECV of apramycin against E. coli was recommended to be 16 µg/mL.

Antibiotic Resistance Profiles, Molecular Mechanisms and Innovative Treatment Strategies of Acinetobacter baumannii

Antibiotic resistance is one of the biggest challenges for the clinical sector and industry, environment and societal development. One of the most important pathogens responsible for severe nosocomial infections is Acinetobacter baumannii, a Gram-negative bacterium from the Moraxellaceae family, due to its various resistance mechanisms, such as the β-lactamases production, efflux pumps, decreased membrane permeability and altered target site of the antibiotic. The enormous adaptive capacity of A. baumannii and the acquisition and transfer of antibiotic resistance determinants contribute to the ineffectiveness of most current therapeutic strategies, including last-line or combined antibiotic therapy. In this review, we will present an update of the antibiotic resistance profiles and underlying mechanisms in A. baumannii and the current progress in developing innovative strategies for combating multidrug-resistant A. baumannii (MDRAB) infections.

Carbapenem-Resistant Enterobacterales: Considerations for Treatment in the Era of New Antimicrobials and Evolving Enzymology

Purpose of Review

Gram-negative resistance is a growing concern globally. Enterobacterales, formerly Enterobacteriaceae, have developed resistance mechanisms to carbapenems that leave very few antimicrobial options in the clinician’s armamentarium.

Recent Findings

New antimicrobials like ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, cefiderocol, and plazomicin have the potential to overcome resistance mechanisms in Enterobacterales including different classes of carbapenemases.

Summary

Novel β-lactam/β-lactamase inhibitors, plazomicin, and cefiderocol give the clinician options that were once not available. Utilizing these options is of the utmost importance when treating carbapenem-resistant Enterobacterales.

High distribution of 16S rRNA methylase genes rmtB and armA among Enterobacter cloacae strains isolated from an Ahvaz teaching hospital, Iran

The emergence of 16S rRNA methylase genes encoded on plasmids confers high-level aminoglycoside resistance (HLAR). This study aimed to investigate the prevalence of 16S rRNA methylases among Enterobacter cloacae strains isolated from an Ahvaz teaching hospital, Iran. A total of 68 E. cloacae clinical strains were collected between November 2017 and September 2018. The MICs of aminoglycosides were assessed using the agar dilution method. The presence of 16S rRNA methylase genes, including armA, rmtA to rmtH, and nmpA was evaluated by PCR. The transferability of 16S rRNA methylase-harboring plasmids was evaluated by conjugation assay. The genetic diversity of all isolates was evaluated by ERIC-PCR. The armA and rmtB genes were the only 16S rRNA methylase genes detected in this study (29 out of 68 isolates; 42.64%). The transferability by conjugation was observed in 23 rmtB or/and armA positive donors. HLAR phenotype was in 33 of 68 strains. Ten clonal types were obtained by ERIC-PCR and significant associations (p < 0.05) were between the clone types and aminoglycoside susceptibility, as well as with profile of the 16S rRNA methylase genes. In conclusion, both horizontal transfer and clonal spread are responsible for dissemination of the rmtB and armA genes among E. cloacae strains.

Emergence of antibiotic resistance Pseudomonas aeruginosa in intensive care unit; a critical review

The emergence of antibiotic resistant bacteria in the healthcare is a serious concern. In the Healthcare premises precisely intensive care unit are major sources of microbial diversity. Recent findings have demonstrated not only microbial diversity but also drug resistant microbes largely habitat in ICU. Pseudomonas aeruginosa found as a part of normal intestinal flora and a significant pathogen responsible for wide range of ICU acquired infection in critically ill patients. Nosocomial infection associated with this organism including gastrointestinal infection, urinary tract infections and blood stream infection. Infection caused by this organism are difficult to treat because of the presence of its innate resistance to many antibiotics (β-lactam and penem group of antibiotics), and its ability to acquire further resistance mechanism to multiple class of antibiotics, including Beta-lactams, aminoglycosides and fluoroquinolones. In the molecular evolution microbes adopted several mechanism to maintain genomic plasticity. The tool microbe use for its survival is mainly biofilm formation, quorum sensing, and horizontal gene transfer and enzyme promiscuity. Such genomic plasticity provide an ideal habitat to grow and survive in hearse environment mainly antibiotics pressure. This review focus on infection caused by Pseudomonas aeruginosa, its mechanisms of resistance and available treatment options. The present study provides a systemic review on major source of Pseudomonas aeruginosa in ICU. Further, study also emphasizes virulence gene/s associated with Pseudomonas aeruginosa genome for extended drug resistance. Study gives detailed overview of antibiotic drug resistance mechanism.

Aminoglycoside Revival: Review of a Historically Important Class of Antimicrobials Undergoing Rejuvenation

Aminoglycosides are cidal inhibitors of bacterial protein synthesis that have been utilized for the treatment of serious bacterial infections for almost 80 years. There have been approximately 15 members of this class approved worldwide for the treatment of a variety of infections, many serious and life threatening. While aminoglycoside use declined due to the introduction of other antibiotic classes such as cephalosporins, fluoroquinolones, and carbapenems, there has been a resurgence of interest in the class as multidrug-resistant pathogens have spread globally. Furthermore, aminoglycosides are recommended as part of combination therapy for empiric treatment of certain difficult-to-treat infections. The development of semisynthetic aminoglycosides designed to overcome common aminoglycoside resistance mechanisms, and the shift to once-daily dosing, has spurred renewed interest in the class. Plazomicin is the first new aminoglycoside to be approved by the FDA in nearly 40 years, marking the successful start of a new campaign to rejuvenate the class.

The role of therapy with aminoglycoside in the outcomes of kidney transplant recipients infected with polymyxin- and carbapenem-resistant Enterobacteriaceae

Kidney transplant recipients are at risk for infections due to carbapenem-resistant Enterobacteriaceae (CRE). Polymyxin-resistant CRE (PR-CRE) infections are especially difficult to treat. The aim of this study was to characterize PR-CRE infections among kidney transplant recipients and identify risk factors for treatment failure. This retrospective cohort study involved all kidney transplant recipients with PR-CRE infection between 2013 and 2017 at our center. Minimal inhibitory concentrations for polymyxin B were determined by broth microdilution. Carbapenem-resistant genes (bla_KPC, bla_NDM, and bla_OXA-48), aminoglycoside-resistance genes, and polymyxin-resistant gene mcr-1 were identified by polymerase chain reaction. All but one of the 47PR-CRE infections identified were due to Klebsiella pneumoniae. The most common type of infection (in 54.3%) was urinary tract infection (UTI). Monotherapy was used in 10 cases. Combined treatment regimens included double-carbapenem therapy in 19 cases, oral fosfomycin in 19, and amikacin in 13. Treatment failure occurred in 21 cases (45.7%). Clinical success was achieved 78.9% of patients who used aminoglycosides versus 37.0% of those who not used this drug (p = 0.007). Multivariate analysis showed diabetes mellitus to be a risk factor for treatment failure; amikacin use and UTI were found to be protective. Nine strains were RmtB producers. Although aminoglycosides constitute an important therapeutic option for PR-CRE infection, the emergence of aminoglycoside resistance could have a major impact on the management of CRE infection.

High-level aminoglycoside resistance in Acinetobacter baumannii recovered from Intensive Care Unit patients in Northeastern India

Background

Acinetobacter baumannii has emerged as an important nosocomial pathogen, its ability to acquire resistance to carbapenems and aminoglycosides, has complicated their treatment regimen. The present study investigates the prevalence and diversity of aminoglycoside-modifying enzymes and 16S methyltransferases in A. baumannii isolates recovered from patients admitted in Intensive Care Unit (ICU) of a tertiary referral hospital in Northeastern India.

Materials and Methods

We investigated the high-level aminoglycoside-resistance (HLAR) (gentamicin and amikacin minimum inhibitory concentration ≥ 512 μg/ml) among 164 multidrug-resistant A. baumannii obtained from ICU. Genes encoding aminoglycoside-modifying enzymes, 16S methyltransferase and coexisting beta-lactamases were amplified. Horizontal transferability, plasmid stability and elimination assays were performed. Clonality and sequence types were evaluated by repetitive extragenic palindromic-polymerase chain reaction and multilocus sequence typing (MLST) respectively.

Results

A total of 130 (79.2%) isolates were found to exhibit HLAR, with acquired aminoglycoside-resistance genes in 109 (83.8%) isolates along with coexisting extended-spectrum beta-lactamases and metallo-beta-lactamases. Genes aph (3') I, aph (3') VIa and armA were predominant and horizontally transferable. Plasmids were eliminated with single sodium dodecyl sulphate treatment. Seventeen haplotypes were found responsible for the infection. MLST revealed circulation of ST583 and ST188 in ICU.

Conclusions

This study reveals the presence of aminoglycoside-resistance genes in combination with bla_CTXM and bla_NDM, which are highly stable and not frequently reported from this geographical region. Further, the study could predict limited treatment option and need for formulating infection control strategy.

NDM-1- and OXA-23-producing Acinetobacter baumannii isolated from intensive care unit patients in Tunisia

Gastrointestinal colonisation by carbapenem-resistant Acinetobacter baumannii (CRAB) is a critical step before nosocomial infection. This study evaluated CRAB intestinal carriage in patients admitted to a Tunisian ICU and determined the antimicrobial resistance mechanisms involved. From December 2014 to February 2015, all 63 patients admitted to the ICU were screened for rectal CRAB colonisation upon admission and once weekly thereafter. ICU patients who acquired a CRAB nosocomial infection were also included. β-Lactamases and associated resistance genes were screened by PCR sequencing, and molecular typing was performed by PFGE and MLST. The CRAB faecal carriage rate at admission was 4.8% (3/63). The CRAB acquisition rate during ICU stay was analysed in 39 of the remaining 60 patients and the rate of acquired CRAB faecal carriage was 15.4% (6/39); 4 patients also showed an ICU-acquired CRAB infection (one patient was a faecal carrier and suffered infection). Overall, 13 CRAB isolates were collected from 12 patients, of which 11 isolates showed resistance to all antibiotics tested except colistin. bla_OXA-23 and bla_NDM-1 were detected in 11 and 2 isolates, respectively. All OXA-23-producing strains carried armA, tetB, sul1 and catB, and some of them carried aph(3')-VIa, bla_TEM-1, aph(3')-Ia and ant(2'')-Ia. The bla_NDM-1-positive isolates harboured aph(3')-VIa and catB. Three PFGE patterns and two STs were identified [ST195 (n = 11), ST1089 (n = 2, NDM-1-positive)]. Whether imported or acquired during ICU stay, CRAB colonisation is a major risk factor for the occurrence of serious nosocomial infection. Systematic screening of faecal carriage is mandatory to prevent their spread.

Emergence of rmtC and rmtF 16S rRNA methyltransferase in clinical isolates of Pseudomonas aeruginosa

Occurrence of aminoglycoside (AG) resistance in clinical isolates of Pseudomonas aeruginosa is investigated in this study. Antimicrobial susceptibility test and minimum inhibitory concentration (MIC) for amikacin and gentamicin were performed followed by polymerase chain reaction amplifications of AG modifying enzyme genes (aac(6´)-I, aac(6´)-II, aac(3)-II/VI, ant(2´´)-I, aph(3´)-VI) and 16S methylases (rmtA-D, rmtF and armA). MIC50and MIC90were 64, 128 and > 256, >256 for amikacin and gentamicin, respectively. Four types of genes (aac(6´)-I, aac(3)-II/VI, ant(2´´)-I and aph(3´)-VI) were found in 53 (57.6%) isolates. ant(2´´)-I was the most predominant gene (28 isolates) followed by aac(6´)-I (23 isolates). Nineteen (20.6%) isolates were positive for 16S RMTases (rmtB, rmtC, rmtF and armA) and two isolates co-harboured rmtB + rmtC + rmtF.

Characterization of Resistance Patterns and Detection of Apramycin Resistance Genes in Escherichia coli Isolated from Chicken Feces and Houseflies after Apramycin Administration

The aim of this study was to evaluate the influence of apramycin administration on the development of antibiotic resistance in Escherichia coli (E. coli) strains isolated from chicken feces and houseflies under field conditions. Chickens in the medicated group (n = 25,000) were given successive prophylactic doses (0.5 mg/l) of apramycin in their drinking water from Days 1 to 5, while no antibiotics were added to the un-medicated groups drinking water (n = 25,000). Over 40 days, a total of 1170 E. coli strains were isolated from fecal samples obtained from medicated and un-medicated chickens and houseflies from the same chicken farm. Apramycin MIC90 values for E. coli strains obtained from the medicated group increased 32-128 times from Days 2 to 6 (256-1024 μg/ml) when compared to those on Day 0 (8 μg/ml). Strains isolated from un-medicated chickens and houseflies had consistently low MIC90 values (8-16 μg/ml) during the first week, but showed a dramatic increase from Days 8 to 10 (128-1024 μg/ml). The apramycin resistance gene aac(3)-IV was detected in E. coli strains from medicated (n = 71), un-medicated (n = 32), and housefly groups (n = 42). All strains positive for aac(3)-IV were classified into 12 pulsed-field gel electrophoresis (PFGE) types. PFGE types A, E, and G were the predominant types in both the medicated and housefly groups, suggesting houseflies play an important role in spreading E. coli-resistant strains. Taken together, our study revealed that apramycin administration could facilitate the occurrence of apramycin-resistant E. coli and the apramycin resistance gene acc(3)-IV. In turn, these strains could be transmitted by houseflies, thus increasing the potential risk of spreading multi-drug-resistant E. coli to the public.

RAPD PCR Profile, Antibiotic Resistance, Prevalence of armA Gene, and Detection of KPC Enzyme in Klebsiella pneumoniae Isolates

The increasing prevalence of multidrug-resistant Klebsiella pneumoniae strains isolated from hospitals shows the limitation of recent antibiotics used for bacterial eradication. In this study, 81 K. pneumoniae isolates were collected from three hospitals in Tehran. Antibiotic susceptibility test showed the highest rates of resistance to cefotaxim (85.5%) and ceftazidime (78.3%), and the lowest rates of resistance were detected for colistin (16.9%), streptomycin (16.8%), and chloroamphenicol (21.7%). Eleven different resistance patterns were observed. Sixty-six out of 81 isolates (81.5%) were found to be multidrug resistant (MDR), and 35.8% of them belonged to A3 resistance pattern. 7.4% and 66.7% were KPC enzyme and armA gene positive, respectively. RAPD PCR assay of these bacteria showed 5 clusters, 16 single types, and 14 common types, and there was not any correlation between genetic patterns of the isolates and presence of resistance agents. Simultaneous detection of resistance-creating agents could be an important challenge for combination therapy of MDR K. pneumoniae-caused infections.

A culture medium for screening 16S rRNA methylase-producing pan-aminoglycoside resistant Gram-negative bacteria

The amikacin plus gentamicin-containing SuperAminoglycoside medium was developed for screening multiple-aminoglycoside resistance in Gram-negative bacteria (Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii). It was evaluated using aminoglycoside-susceptible (n=12) and aminoglycoside-resistant (n=59) Gram-negative isolates, including 16S rRNA methylase producers (n=20). Its sensitivity and specificity of detection were, respectively, of 95% and 96% for detecting multiple aminoglycoside-resistant methylase producers.

New eight genes identified at the clinical multidrug-resistant Acinetobacter baumannii DMS06669 strain in a Vietnam hospital

Background

Acinetobacter baumannii is an important nosocomial pathogen that can develop multidrug resistance. In this study, we characterized the genome of the A. baumannii strain DMS06669 (isolated from the sputum of a male patient with hospital-acquired pneumonia) and focused on identification of genes relevant to antibiotic resistance.

Methods

Whole genome analysis of A. baumannii DMS06669 from hospital-acquired pneumonia patients included de novo assembly; gene prediction; functional annotation to public databases; phylogenetics tree construction and antibiotics genes identification.

Results

After sequencing the A. baumannii DMS06669 genome and performing quality control, de novo genome assembly was carried out, producing 24 scaffolds. Public databases were used for gene prediction and functional annotation to construct a phylogenetic tree of the DMS06669 strain with 21 other A. baumannii strains. A total of 18 possible antibiotic resistance genes, conferring resistance to eight distinct classes of antibiotics, were identified. Eight of these genes have not previously been reported to occur in A. baumannii.

Conclusions

Our results provide important information regarding mechanisms that may contribute to antibiotic resistance in the DMS06669 strain, and have implications for treatment of patients infected with A. baumannii.

Electronic supplementary material

The online version of this article (10.1186/s12941-017-0250-9) contains supplementary material, which is available to authorized users.

Plasmids of Diverse Inc Groups Disseminate the Fosfomycin Resistance Gene fosA3 among Escherichia coli Isolates from Pigs, Chickens, and Dairy Cows in Northeast China

Thirty-nine fosfomycin-resistant Escherichia coli isolates carrying fosA3 were obtained from pigs, chickens, dairy cows, and staff in four northeastern provinces of China between June 2015 and April 2016. The fosA3 gene was colocated with bla_CTX-M genes on conjugative plasmids of the incompatibility groups IncN (n = 12), IncN-F33:A^-:B^-(n = 2), IncF33:A^-:B^-(n = 14), IncF14:A^-:B^-(n = 2), and IncI1/sequence type 136 (ST136) (n = 9). Four different genetic contexts of fosA3 were detected among the 39 E. coli isolates. Three potential epidemic plasmids circulated among E. coli strains from this region.

Drug-resistant gram-negative uropathogens: A review

Urinary tract infection(UTI) caused by Gram-negative bacteria is the second most common infectious presentation in community medical practice. Approximately 150 million people are diagnosed with UTI each year worldwide. Drug resistance in Gram-negative uropathogens is a major global concern which can lead to poor clinical outcomes including treatment failure, development of bacteremia, requirement for intravenous therapy, hospitalization, and extended length of hospital stay. The mechanisms of drug resistance in these bacteria are important due to they are often not identified by routine susceptibility tests and have an exceptional potential for outbreaks. Treatment of UTIs depends on the access to effective drugs, which is now threatened by antibiotic resistant Gram-negative uropathogens. Although several effective antibiotics with activity against highly resistant Gram-negatives are available, there is not a unique antibiotic with activity against the high variety of resistance. Therefore, antimicrobial susceptibility tests, correlation between clinicians and laboratories, development of more rapid diagnostic methods, and continuous monitoring of drug resistance are urgent priorities. In this review, we will discuss about the current global status of drug-resistant Gram-negative uropathogens and their mechanisms of drug resistance to provide new insights into their treatment options.

Clonal replacement of epidemic KPC-producing Klebsiella pneumoniae in a hospital in China

BACKGROUND

Klebsiella pneumoniae is a frequent nosocomial pathogen causing difficult-to-treat infections worldwide. The prevalence of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-KP) is increasing in China. The aim of this study was to investigate the molecular epidemiology of KPC-KP in a nosocomial outbreak.

METHODS

Fifty-four KPC-KP isolates were consecutively collected between November 2013 and August 2014 during a KPC-KP outbreak in a tertiary care hospital in Beijing, China. Antimicrobial susceptibility was determined by agar dilution. Carbapenemase, extended-spectrum β-lactamase, 16S rRNA methylase, AmpC β-lactamase, and plasmid-mediated quinolone resistance determinants were detected by PCR amplification. The genetic relatedness of isolates was analyzed by pulsed-field gel electrophoresis and multi-locus sequence typing.

RESULTS

All isolates belonged to ST11 except one isolate which was identified as a new sequence type (ST2040). PFGE profile of genomic DNA revealed seven clusters, of which cluster A and C dominated the KPC-KP outbreak and cluster A was replaced by cluster C during the outbreak. PFGE of genomic DNA, S1-PFGE of plasmids, replicon typing, and drug resistant characteristics showed that clonal spread occurred during the outbreak. When compared with isolates within cluster A, all isolates in cluster C harbored rmtB and showed higher level of resistance to cefepime, amikacin, tobramycin, and tigecycline.

CONCLUSION

We reported a nosocomial outbreak of KPC-KP with clonal replacement and a new sequence type (ST2040) of KP. High degree of awareness and surveillance of KPC-KP should be given to avoid potential outbreaks, especially in ICU wards.

Rapid Aminoglycoside NP Test for Rapid Detection of Multiple Aminoglycoside Resistance in Enterobacteriaceae

The rapid aminoglycoside NP (Nordmann/Poirel) test was developed to rapidly identify multiple aminoglycoside (AG) resistance in Enterobacteriaceae It is based on the detection of the glucose metabolism related to enterobacterial growth in the presence of a defined concentration of amikacin plus gentamicin. Formation of acid metabolites was evidenced by a color change (orange to yellow) of the red phenol pH indicator. The rapid aminoglycoside NP test was evaluated by using bacterial colonies of 18 AG-resistant isolates producing 16S rRNA methylases, 20 AG-resistant isolates expressing AG-modifying enzymes (acetyl-, adenyl-, and phosphotransferases), and 10 isolates susceptible to AG. Its sensitivity and specificity were 100% and 97%, respectively, compared to the broth dilution method, which was taken as the gold standard for determining aminoglycoside resistance. The test is inexpensive, rapid (<2 h), and implementable worldwide.

Proteomic Analyses Uncover the Mechanisms Underlying Antibiotic Resistance Differences among Three Acinetobacter baumannii Isolates

This study aimed to investigate the molecular mechanisms underlying the antibiotic resistance difference among three Acinetobacter baumannii isolates. Fifty A. baumannii isolates were first subjected to an antimicrobial susceptibility test, then three isolates differing in antibiotic resistance were selected and subjected to iTRAQ (isobaric tags for relative and absolute quantification)-based proteomics analysis. Differential proteins among the three A. baumannii isolates were further identified and subjected to gene ontology functional enrichment analysis. A resistant isolate (A1), a less resistant one (A8) and a susceptible one (A9) were selected. In total, there were 424 differentially expressed proteins (DEPs) between the A1 and A8 isolates, 1,992 DEPs between the A9 and A1 isolates, and 1,956 DEPs between the A8 and A9 isolates. The upregulation of I6TUC8 and Q0GA83 in the A1 and A8 isolates may be responsible for their higher resistance to ceftriaxone. The higher gentamicin resistance of A. baumannii isolates A1 and A8 when compared to A9 may be related to the higher expression levels of O05286 and D0CCK1, while the higher Q2FCY1 expression level may contribute more to strong gentamicin resistance in A1. The higher levels of L9LWL7, L9MDB0, K9C9W3, E2IGU7, B6E129, G8HYR7, D2XTB0 and D2XTB0 may be responsible for the higher carbapenem resistance of isolate A1 as compared to A8.

Epidemiology and virulence of VIM-4 metallo-beta-lactamase-producing Pseudomonas aeruginosa isolated from burn patients in eastern Algeria

In this study, we investigated the prevalence of carbapenem-resistant Pseudomonas aeruginosa (CRPA) in burn patients from eastern Algeria, CRPA virulence factors and the molecular epidemiology of CRPA. The overall prevalence of CRPA was 48.38%. Seven (46.66%) isolates were metallo-β-lactamases (MBL) producers and contained the MBL genes blaVIM-4 (n=6) and blaVIM-2 (n=1). Risk factors for CRPA infection were urinary catheter use and intubation (p=0.008). A high percentage of virulence factors (86.6% of these isolates were able to produce protease; 73.3% of isolates has DNase; and 66.6% were haemolysin positive) was observed in CRPA isolates. Among the seven MBL-producing isolates, four had the same clonal profile. The class 1 integrons, which contained the aadA7 gene cassette, were detected in six isolates. The 16SrRNA methylase gene, rmtB, was detected in one strain. All CRPA isolates were biofilm formers. A study on the kinetics of biofilm production revealed that biofilm production increased when the concentration of imipenem or ciprofloxacin and the incubation time increased. This is the first study to report the presence of VIM-4-producing P. aeruginosa from North Africa and also of the high prevalence of CRPA isolates. Based on our study of burn unit patients, the high percentage of P. aeruginosa with virulence factors and multi-drug resistance is alarming.

Aminoglycoside Resistance in Clinical Isolates of Gram Negative Bacilli at the University Hospital of the West Indies, Jamaica: Comparison of Two Time Periods

OBJECTIVE

Aminoglycosides were introduced into use over 60 years ago. The University Hospital of the West Indies (UHWI), a tertiary care teaching hospital, in Kingston, Jamaica, introduced the use of gentamicin in 1973 and amikacin in 1980. This report examined the susceptibility patterns to these agents in 1547 consecutive isolates of Gram negative bacilli (GNB) encountered between September 1 and November 30, 2011, at UHWI and compares the data with those observed previously in 1981 at the same institution.

METHODS

The Vitek 2 (bioMeriéux, Durham, NC) was used for isolate identification, minimum inhibitory concentration determination and aminoglycoside susceptibility testing. Quality control was done using American Type Culture Collection standard strains of E coli (ATCC 25922) and Pseudomonas aeruginosa (ATCC 27853).

RESULTS

Of the 1547 organisms, 267 had resistance to one or both aminoglycosides. Amikacin resistance increased from 0.6% (1981) to 7.2% [2011] (p < 0.05), while gentamicin resistance increased from 6.7% to 14.8% (p < 0.05) for the corresponding period. The majority of samples with aminoglycoside resistant organisms came from the intensive care unit and surgical inpatients. Urine samples persistently produced the largest amount of gentamicin resistant isolates.

CONCLUSIONS

Although there has been a statistically significant rise in aminoglycoside resistance, aminoglycosides continue to remain highly effective against approximately 83% of GNB despite continuous usage at this institution for over three decades. Continued national surveillance, implementation of infection control policies and antibiotic stewardship are all essential in retaining low resistance levels.

Epidemiology of carbapenem non-susceptible Pseudomonas aeruginosa isolates in Eastern Algeria

Background

Carbapenem resistance among Pseudomonas aeruginosa has become a serious life-threatening problem due to the limited therapeutic options. In this study, we investigated the prevalence and the molecular epidemiology of carbapenem resistant Pseudomonas aeruginosa (CRPA) isolated from three hospitals in Annaba city, Algeria.

Methods

During the study period (January, 2012 to December, 2013), all patients infected by P. aeruginosa were considered as the potential study population. Antibiotic susceptibility testing was performed as recommended by the CLSI. Screening of carbapenemase producer isolates was performed by using imipenem-EDTA double-disk synergy test and modified Hodge test. CRPA isolates were tested for the presence of genes encoding β-lactamases, plasmid mediated quinolone resistance, aminoglycoside resistance and class 1 integrons were investigated by PCR and sequencing. The clonal relatedness among CRPA isolates was analyzed by pulsed-field gel electrophoresis method. The clinical data were collected to identify risk factors for CRPA carriage of P. aeruginosa infection.

Results

The overall prevalence of CRPA was 18.75 %. The risk factors for carrying CRPA were the length of hospital stay (p = 0.04), co-infections with Staphylococcus aureus (p = 0.01), and the use of urinary catheter (p = 0.03). The in-hospital mortality rate among case patients was 13.33 % compared with 1.53 % for control patients (p = 0.09). All CRPA isolates were multidrug resistance and the most effective antibiotic against CRPA isolates was amikacin and colistin. PFGE revealed an epidemic clonal dissemination of CRPA isolates. None of CRPA isolated were found to be carbapenemase-producers. The bla_PSE-1 and aac(3)-II gene was detected in two and five strains respectively. The class1 integrons were detected in 2 isolates with the presence of aadA7 gene cassette in these integrons.

Conclusion

The endemic clonal dissemination and multi-drug resistance of CRPA isolates in our institution is highly alarming. Strict measure will be required to control the further spread of these pathogens in hospital setting.

Amphiphilic Aminoglycoside Antimicrobials in Antibacterial Discovery

Amphiphilic aminoglycoside antimicrobials (AAAs) are an emerging class of polycationic antibacterial agents with broad-spectrum antibacterial activity. In contrast to aminoglycosides, which interfere with protein synthesis by interacting with the 30S ribosomal subunit, AAAs appear to target the bacterial cell wall by interactions with extracellular lipids or proteins or by enhancing the permeability of the bacterial cell wall. The physicochemical similarities between amphiphilic aminoglycosides and antimicrobial peptides, another class of polycationic amphiphiles with broad-spectrum antibacterial activity, suggest similar mode(s) of action. However, in contrast to antimicrobial peptides, AAAs are not composed of peptide bonds and as such promise to display superior metabolic stability. As a result, AAAs may be considered to be a novel class of antimicrobial peptidomimetics. Many AAAs possess impressive potent antibacterial activity against Gram-positive and Gram-negative bacteria, especially against bacterial strains that are resistant to clinically used antibiotics. In summary, AAAs promise to provide a new and rich source of antibacterial lead structures to combat antibiotic-resistant and multidrug-resistant pathogens.

Genetic basis of high level aminoglycoside resistance in Acinetobacter baumannii from Beijing, China

The objective of this study was to investigate the genetic basis of high level aminoglycoside resistance in Acinetobacter baumannii clinical isolates from Beijing, China. 173 A. baumannii clinical isolates from hospitals in Beijing from 2006 to 2009 were first subjected to high level aminoglycoside resistance (HLAR, MIC to gentamicin and amikacin>512 µg/mL) phenotype selection by broth microdilution method. The strains were then subjected to genetic basis analysis by PCR detection of the aminoglycoside modifying enzyme genes (aac(3)-I, aac(3)-IIc, aac(6')-Ib, aac(6')-II, aph(4)-Ia, aph(3')-I, aph(3')-IIb, aph(3')-IIIa, aph(3')-VIa, aph(2″)-Ib, aph(2″)-Ic, aph(2″)-Id, ant(2″)-Ia, ant(3″)-I and ant(4')-Ia) and the 16S rRNA methylase genes (armA, rmtB and rmtC). Correlation analysis between the presence of aminoglycoside resistance gene and HLAR phenotype were performed by SPSS. Totally 102 (58.96%) HLAR isolates were selected. The HLAR rates for year 2006, 2007, 2008 and 2009 were 52.63%, 65.22%, 51.11% and 70.83%, respectively. Five modifying enzyme genes (aac(3)-I, detection rate of 65.69%; aac(6')-Ib, detection rate of 45.10%; aph(3')-I, detection rate of 47.06%; aph(3')-IIb, detection rate of 0.98%; ant(3″)-I, detection rate of 95.10%) and one methylase gene (armA, detection rate of 98.04%) were detected in the 102 A. baumannii with aac(3)-I+aac(6')-Ib+ant(3″)-I+armA (detection rate of 25.49%), aac(3)-I+aph(3')-I+ant(3″)-I+armA (detection rate of 21.57%) and ant(3″)-I+armA (detection rate of 12.75%) being the most prevalent gene profiles. The values of chi-square tests showed correlation of armA, ant(3″)-I, aac(3)-I, aph(3')-I and aac(6')-Ib with HLAR. armA had significant correlation (contingency coefficient 0.685) and good contingency with HLAR (kappa 0.940). The high rates of HLAR may cause a serious problem for combination therapy of aminoglycoside with β-lactams against A. baumannii infections. As armA was reported to be able to cause high level aminoglycoside resistance to most of the clinical important aminoglycosides (gentamicin, amikacin, tobramycin, etc), the function of aminoglycoside modifying enzyme gene(s) in A. baumannii carrying armA deserves further investigation.

Prevalence of 16S rRNA methylase genes among β-lactamase-producing Enterobacteriaceae clinical isolates in Saudi Arabia

BACKGROUND

Co production of 16S rRNA methylases gene and β-Lactamase gene among Enterobacteriaceae isolates conferring resistance to both therapeutic options has serious implications for clinicians worldwide.

METHODS

To study co existence of 16S rRNA methylases (armA, rmtA, rmtB, rmtC, rmtD, and npmA) and β-Lactamase (blaTEM-1, blaSHV-12, blaCTX-M-14) genes, we screened all phenotypic positive β-Lactamase producing enterobacteriaceae by polymerase chain reaction (PCR) targeting above genes. A total of 330 enterobacteriaceae strains were collected during study period out of that 218 isolates were identified phenotypically as β-Lactamase producers, which include 50 (22.9%) Escherichia coli; 92 (42.2%) Klebsiella pneumoniae, 44 (20.2%), Citrobactor freundii and 32 (14.7%) Enterobacter spp.

RESULTS

Among this 218, only 188 isolates harbored the resistant gene for β-Lactamase production. Major β-Lactamase producing isolates were blaTEM-1 type. 122 (56 %) isolates were found to produce any one of the 16S rRNA methylase genes. A total of 116 isolates co produced b-Lactamase and at least one 16S rRNA methylases gene Co production of armA gene was found in 26 isolates with rmtB and in 4 isolates with rmtC. The rmtA and rmtD genes were not detected in any of the tested isolates. Six isolates were positive for a 16S rRNA methylase gene alone.

CONCLUSION

β-Lactamase producing isolates appears to coexist with 16S rRNA methylase predominantly armA and rmtB genes in the same isolate. We conclude the major β-Lactamase and 16S rRNA methylases co-producer was K. pneumoniae followed by E. coli. We suggest further work on evaluating other β-lactamases types and novel antibiotic resistance mechanisms among Enterobacteriaceae.

Comparison of plasmids coharboring 16s rrna methylase and extended-spectrum β-lactamase genes among Escherichia coli isolates from pets and poultry

A total of 247 Escherichia coli isolates (148 from diseased or dead poultry and 99 from diseased pets in the People's Republic of China) were screened for extended-spectrum β-lactamase (ESBL) determinants by PCR and sequencing. Then, 16S rRNA methylase genes were detected among ESBL-producing isolates. Clonal relatedness of the E. coli isolates was examined by pulsed-field gel electrophoresis. Conjugation experiments were performed to investigate the association of 16S rRNA methylases and ESBLs, and plasmid contents were also characterized. Among 247 E. coli isolates, 74 (29.96%) isolates were positive for blaCTX-M genes, 42 from pets (12 from cats and 30 from dogs) and 32 from poultry (12 from chickens and 20 from ducks). The most common CTX-M type in isolates from pets was blaCTX-M-14, whereas blaCTX-M-27 was the most common for poultry. rmtB was dectected in 39 of the 74 blaCTX-M-positive isolates, 18 from pets and 21 from poultry. One strain from a pet was found to harbor blaCTX-M-14, blaCTX-M-15, and rmtB. blaCTX-M and rmtB were found to be colocated on the same transferable plasmid in 16 isolates. These genes were on the same or similar plasmids (eight F2:A-:B- and two IncN) in isolates from ducks, whereas they were colocated on the similar F2:A-:B- or similar F33:A-:B- plasmids in isolates of pets origin. In conclusion, similar F2:A-:B- plasmids and similar F33:A-:B- plasmids are responsible for the dissemination of both rmtB and blaCTX-Mgenes in E. coli isolates from poultry and pets, respectively.

Prevalence and molecular epidemiology of plasmid-mediated fosfomycin resistance genes among blood and urinary Escherichia coli isolates

A total of 1878 non-duplicate clinical Escherichia coli isolates (comprising 1711 urinary isolates and 167 blood-culture isolates), which were collected from multiple centres in Hong Kong during 1996-2008, were used to investigate the prevalence and molecular epidemiology of plasmid-mediated fosfomycin (fos) resistance genes. Eighteen of the 1878 clinical E. coli isolates were fosfomycin resistant, of which six were fosA3 positive and two were positive for another fosA variant (designated fosKP96). No isolates had the fosC2 gene. The clones of the eight isolates were diverse: sequence type (ST) 95 (n = 2), ST118 (n = 1), ST131 (n = 1), ST617 (n = 1), ST648 (n = 1), ST1488 (n = 1) and ST2847 (n = 1). In the isolates, fosA3 and blaCTX-M genes were co-harboured on conjugative plasmids with F2:A-:B- (n = 2), N (n = 1), F-:A-:B1 and N (n = 1) and untypable (n = 2) replicons. Both fosKP96-carrying plasmids belonged to replicon N. RFLP analysis showed that the two F2:A-:B- plasmids carrying fosA3 and blaCTX-M-3 genes shared the same pattern. Complete sequencing of one of the two F2:A-:B- plasmids, pFOS-HK151325 (69 768 bp) demonstrated it to be >99 % identical to the previously sequenced plasmid pHK23a originating from a pig E. coli isolate in the same region. This study demonstrated the dissemination of fosA3 genes in diverse E. coli clones on multiple blaCTX-M-carrying plasmid types, of which F2:A-:B- plasmids closely related to pHK23a were shared by isolates from human and animal sources.

The clinical impact of multidrug-resistant gram-negative bacilli in the management of septic shock

Multi-antibiotic drug-resistant (MDR) gram-negative bacilli are becoming a major threat to the standard care of septic patients. Empiric antimicrobial drug regimens to cover likely bacterial pathogens have to be altered in keeping with the spread of MDR pathogens in the health care setting and in the community. Reliable antibiotics for broad spectrum coverage for sepsis such as extended spectrum β-lactam antibiotics, carbapenems, and fluoroquinolones can no longer be counted upon to provide activity against a range of common, virulent pathogens that cause sepsis. In some regions of Asia, South America, and Eastern Europe in particular, MDR pathogens have become a major concern, necessitating the use of potentially toxic and costly antibiotic combinations as initial antibiotic therapy for septic shock. In this brief review, we will focus on the emergence of MDR gram-negative pathogens, resistance mechanisms, and suggest some management and prevention strategies against MDR pathogens.

Nosocomial infection by sequence type 357 multidrug-resistant Acinetobacter baumannii isolates in a neonatal intensive care unit in Daejeon, Korea

Acinetobacter baumannii is an important microorganism responsible for a number of nosocomial outbreaks, in particular, in intensive care units (ICUs). We investigated a nosocomial infection caused by multidrug-resistant (MDR) A. baumannii in a neonatal intensive care unit (NICU) in Korea. A. baumannii isolates were characterized using Etest (AB Biodisk, Sweden), two multiplex PCR assays, and multilocus sequence typing (MLST) scheme. PCR and PCR mapping experiments were performed for detecting and characterizing the determinants of antimicrobial resistance. Eight strains isolated from an NICU belonged to European (EU) clone II and revealed only one sequence type (ST), namely, ST357. All the isolates were susceptible to imipenem but were resistant to amikacin, gentamicin, ceftazidime, cefepime, and ciprofloxacin. To the best of our knowledge, this is the first report of a nosocomial infection in an NICU in Korea caused by ST357 MDR/carbapenem-susceptible A. baumannii strains. This result demonstrates that nosocomial outbreaks of MDR/carbapenem-susceptible strains as well as MDR/carbapenem-resistant isolates may occur in NICUs.

Emergence of 16S rRNA methylase-producing Acinetobacter baumannii and Pseudomonas aeruginosa isolates in hospitals in Vietnam

Background

16S rRNA methylase-producing Gram-negative bacteria are highly resistant to all clinically important aminoglycosides. We analyzed clinical strains of 16S rRNA methylase-producing Acinetobactor baumannii and Pseudomonas aeruginosa obtained from clinical isolates in medical settings in Vietnam.

Methods

From 2008 to 2011, 101 clinical strains of A. baumannii and 15 of P. aeruginosa were isolated from patients in intensive care units (ICUs) in two medical settings in Vietnam. Antimicrobial susceptibilities were determined using the microdilution method and epidemiological analysis was performed by pulsed-field gel electrophoresis and MLST. Genes encoding the 16S rRNA methylases, OXAs and CTX-Ms were analyzed by PCR and sequence analysis.

Results

16S rRNA methylase-producing Gram-negative pathogens were detected in two hospitals in Vietnam. Of the 101 clinical isolates of A. baumannii and the 15 of P. aeruginosa isolated from two ICUs in these hospitals, 72 (71.3%) were highly resistant to amikacin, arbekacin and gentamicin, with MICs greater than 1,024 mg/L. The 16S rRNA methylases ArmA and RmtB were produced by 61 and 9 isolates of A. baumannii, respectively, and RmtB was produced by 2 isolates of P. aeruginosa. Moreover, 52 of the A. baumannii isolates producing 16S rRNA methylases harbored both blaOXA-23-like and blaOXA-51-like genes. Most A. baumannii isolates producing 16S rRNA methylase obtained in hospital A in Hanoi were ST91 and ST231, whereas most from hospital B in Ho Chi Minh City were ST136, ST195, and ST254.

The two P. aeruginosa isolates harboring rmtB showed different patterns on PFGE, one each corresponding to ST217 and ST313.

Conclusions

Gram-negative bacteria producing the 16S rRNA methylases ArmA and RmtB are emerging in medical settings in Vietnam. A. baumannii isolates in northern and southern regions of Vietnam may be of different lineages.