blaOXA Genes Research Articles

Occurrence of Carbapenemases, Extended-Spectrum Beta-Lactamases and AmpCs among Beta-Lactamase-Producing Gram-Negative Bacteria from Clinical Sources in Accra, Ghana

Beta-lactamase (β-lactamase)-producing Gram-negative bacteria (GNB) are of public health concern due to their resistance to routine antimicrobials. We investigated the antimicrobial resistance and occurrence of carbapenemases, extended-spectrum β-lactamases (ESBLs) and AmpCs among GNB from clinical sources. GNB were identified using matrix-assisted laser desorption/ionization time of flight–mass spectrometry (MALDITOF-MS). Antimicrobial susceptibility testing was performed via Kirby–Bauer disk diffusion and a microscan autoSCAN system. β-lactamase genes were determined via multiplex polymerase chain reactions. Of the 181 archived GNB analyzed, Escherichia coli and Klebsiella pneumoniae constituted 46% (n = 83) and 17% (n = 30), respectively. Resistance to ampicillin (51%), third-generation cephalosporins (21%), and ertapenem (21%) was observed among the isolates, with 44% being multi-drug resistant (MDR). β-lactamase genes such as AmpCs ((blaFOX-M (64%) and blaDHA-M and blaEDC-M (27%)), ESBLs ((blaCTX-M (81%), other β-lactamase genes blaTEM (73%) and blaSHV (27%)) and carbapenemase ((blaOXA-48 (60%) and blaNDM and blaKPC (40%)) were also detected. One K. pneumoniae co-harbored AmpC (blaFOX-M and blaEBC-M) and carbapenemase (blaKPC and blaOXA-48) genes. blaOXA-48 gene was detected in one carbapenem-resistant Acinetobacter baumannii. Overall, isolates were resistant to a wide range of antimicrobials including last-line treatment options. This underpins the need for continuous surveillance for effective management of infections caused by these pathogens in our settings.

Genome-wide identification and oxacillinase OXA distribution characteristics of Acinetobacter spp. based on a global database.

To use genomic analysis to identify Acinetobacter spp. and to explore the distribution characteristics of ß-lactamase oxallicinases (blaOXA) among Acinetobacter species globally. Genomes of global Acinetobacter spp. were downloaded from GenBank using Aspera batch. After quality check using CheckM and QUAST software, the genomes were annotated using Prokka software to investigate the distribution of blaOXAs across Acinetobacter spp.; a phylogenetic tree was constructed to explore the evolutionary relationship among the blaOXA genes in Acinetobacter spp. Average-nucleotide identification (ANI) was performed to re-type the Acinetobacter spp. BLASTN comparison analysis was implemented to determine the sequence type (ST) of Acinetobacter baumannii strain. A total of 7,853 genomes were downloaded, of which only 6,639 were left for further analysis after quality check. Among them, 282 blaOXA variants were identified from the genomes of 5,893 Acinetobacter spp.; blaOXA-23 (n = 3,168, 53.8%) and blaOXA-66 (2,630, 44.6%) were the most frequent blaOXAs, accounting for 52.6% (3,489/6639), and the co-carriage of blaOXA-23 and blaOXA-66 was seen in 2223 (37.7%) strains. The 282 blaOXA variants were divided into 27 clusters according to the phylogenetic tree. The biggest clade was blaOXA-51-family carbapenem-hydrolyzing enzymes composed of 108 blaOXA variants. Overall, 4,923 A. baumannii were identified out of the 6,639 Acinetobacter spp. strains and 291 distinct STs were identified among the 4,904 blaOXA-carrying A. baumannii. The most prevalent ST was ST2 (n = 3,023, 61.6%) followed by ST1 (n = 228, 4.6%). OXA-like carbapenemases were the main blaOXA-type β-lactamase spread widely across Acinetobacter spp. Both blaOXA-23 and blaOXA-66 were the predominant blaOXAs, among all A. baumannii strains, with ST2 (belonging to CC2) being the main clone disseminated globally.

High Prevalence of Antiseptic Resistance Encoding Genes and Reduced Phenotypic Antiseptic Susceptibility Among Antibiotic-Resistant Pseudomonas aeruginosa Isolates

Background: Multi-drug resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa isolates are of clinical concern. Objectives: To determine the distribution of antiseptic resistance genes and the associated level of phenotypic antiseptic resistance against quaternary ammonium compounds and biguanide compounds, we studied MDR and XDR P. aeruginosa isolates collected from different infections among patients from a single hospital. Methods: Pseudomonas aeruginosa isolates were investigated in 2020 for in vitro susceptibility to benzethonium chloride (BTC), benzalkonium chloride (BKC), and chlorhexidine digluconate (CHG). The minimum inhibitory concentrations (MICs) against these antiseptic agents were determined using broth microdilution. Also, polymerase chain reaction (PCR)-mediated detection of qacE, qacEΔ1, and blaOXA-23 genes was used. Results: Isolates were largely non-clonal according to their phenotypical and genotypical non-similarity (35 overall data-combination types detected). Most P. aeruginosa infections occurred in intensive care unit (ICU) patients (n = 43, 61.4%). Extensively drug-resistant and MDR phenotypes were detected in 20% and 12.6%, respectively. Among the 70 isolates retained, 53 (75.7%) harbored at least one resistance gene, comprising 11 (20.7%) isolates with solely the qacEΔ1 gene; seven (13.2%) isolates harbored the qacE gene. Both the qacE and qacEΔ1 genes were detected simultaneously in 35 (66%) isolates. The mean MICs for BTC (24.0 versus 10.56 µg/mL), BKC (46.1 versus 17.22 µg/mL), and CHG (107.7 versus 29.4 µg/mL) were statistically significantly higher among antiseptic resistance gene harboring isolates than in other isolates without such genes. Conclusions: The significantly increased MICs against antiseptic agents among antibiotic-resistant P. aeruginosa isolates highlight the importance of monitoring such increases and implementing effective infection control.

Prevalence and Phenotypic and Genotypic Patterns of Antibiotic Resistance of Acinetobacter baumannii Strains Isolated from Fish, Shrimp, and Lobster Samples

Acinetobacter baumannii has emerged as a significant hospital pathogen, quickly becoming resistant to commonly prescribed antimicrobials. The present survey was done to evaluate the prevalence, antibiotic resistance pattern, and distribution of antibiotic resistance genes amongst the A. baumannii strains isolated from fish, shrimp, and lobster samples. Four-hundred and fifty seafood samples (100 g each) were collected from Shiraz, Iran. Acinetobacter baumannii was determined using culture and biochemical tests. Pattern of antibiotic resistance and distribution of antibiotic resistance genes were determined using the disk diffusion and polymerase chain reaction, respectively. A. baumannii contamination rate amongst the examined seafood samples was 4.44%, with the higher contamination rate of fish samples (7.85%). A. baumannii isolates harbored the maximum resistance rate against tetracycline (85%), ampicillin (85%), gentamicin (70%), and erythromycin (60%). Resistance rates toward trimethoprim-sulfamethoxazole, ciprofloxacin, ceftazidime, and azithromycin were 55%, 45%, 35%, and 30%, respectively. The minimum rates of resistance were obtained against imipenem (10%) and chloramphenicol (15%). The most commonly detected antibiotic resistance genes were blaCITM (75%), blaSHV (70%), tetA (70%), qnrA (55%), blaVIM (50%), and aac(3)-IV (50%). aadA1, sul1, dfrA1, qnr, blaVIM, blaSIM, blaOXA-51, blaOXA-23, and blaOXA-58 genes were detected in 40%, 30%, 45%, 50%, 35%, 25%, 30%, and 20% of isolates, respectively. The role of seafood samples as a potential reservoirs of antibiotic-resistant A. baumannii strains was determined. However, further investigations are required to identify additional epidemiological features of A. baumannii in seafood samples.

Coexistence Of Blaoxa-48, Blavim, And Blashv Genes In Klebsiella Pneumoniae And Escherichia Coli Isolated From Urinary Tract Infections: Microbiological And Epidemiological Analysis.

To investigate antimicrobial resistance mechanisms of isolated bacterialstrains, and their correlation with virulence profile. The cross-sectional study was conducted in January 2020 at outpatient health centres in Kafrelsheikh Governorate of Egypt, and comprised urine samples from patients regardless of age and gender. Midstream samples were collected into sterile swaps which were kept in ice-cooled boxes until transported to the laboratory within 5h. Antimicrobial resistance profile of the isolated Enterobacteriaceae was done using Kirby-Bauer disk diffusion method and was confirmed withVitek compact 2. The phenotypic of carbapenemases and extended-spectrum beta lactamase was determined, and polymerase chain reaction was used, as appropriate. Data was analysed using SPSS 20. Of the 199 patients, 101(50.7%) were females and 98(49.3%) were males. The majority 73(36.6%) were aged 30-50 years. Urinary tract infection was found in 68(34.2%) patients. In 28(41.2%) of these patients, there were 32 isolates of Enterobacterales; 21(65.62%) Klebsiella pneumoniae, 7(21.87%) Escherichia coli and 4(12.5%) Enterobacter cloacae. Of the 28(41.2%) patients, 24(85.7%) were infected with a single strain; 17(70.8%) Klebsiella pneumoniae, 4(16.7%) Escherichia coli and 3(12.5%) Enterobacter cloacae. In 3(10.7%) cases, there was co-infection with Escherichia coli and Klebsiella pneumoniae, and 1(3.6%)sample had mixed infection with Klebsiella pneumoniae and Enterobacter cloacae. The other 40(58.8%) patients had other causative agents. Housewives, agricultural workers and those aged >50 years had a higher risk of urinary tract infections(p<0.05) Among Klebsiella pneumonia isolates, 6(28.5%) possessed carbapenemase-related genes and 4(19.1%) extended-spectrum beta lactamase-related genes. The carbapenemase related genes were bla-Verona integron-encoded metallo beta lactamase 6(100%) bla-New Delhi metallo beta lactamase-1 4(66.6%) and bla-oxacillinase-48 2(33.3%). The 4(19.1%) cases of extended-spectrum beta lactamase related genes had bla-temoneira gene 3(75%) and bla-sulfhydryl variable gene 4(100%). In Escherichia coli isolates, bla-oxacillinase-48 and bla-Cefotaximase genes were observed in 2(28.5%) cases.Virulence genes uridine diphosphate glucose 4-epimerase, fimbrial adhesion and mannose-resistance adhesin of Klebsiella spp genes in Klebsiella pneumoniae isolates were positive in in 16(76.2%), 14(66.7%) and 10(47.6%) cases, respectively. All 21(100%) isolates of Klebsiella pneumoniae were negative for mucoviscosity-associated gene A. There was evidence of the coexistence of bla- oxacillinase-48, bla-Verona integron-encoded metallo beta lactamase and bla-sulfhydryl variable genes in Klebsiella pneumoniae and Escherichia coli isolates from mixed urinary tract infection samples.

Unveiling the Emergence and Genetic Diversity of OXA-48-like Carbapenemase Variants in Shewanella xiamenensis.

An increase in the carbapenem-hydrolyzing capacity of class D β-lactamase has been observed in strains of multiple species, posing a significant challenge to the control of antibiotic resistance. In this study, we aimed to investigate the genetic diversity and phylogenetic characteristics of new blaOXA-48-like variants derived from Shewanella xiamenensis. Three ertapenem-non-susceptible S. xiamenensis strains were identified, one isolated from the blood sample of an inpatient, the other two isolated from the aquatic environment. Phenotypic characterization confirmed that the strains were carbapenemase producers and exhibited antimicrobial resistance patterns to ertapenem, with some showing lower susceptibility to imipenem, chloramphenicol, ciprofloxacin, and tetracycline. No significant resistance to cephalosporins was observed. Sequence analysis revealed that one strain harbored blaOXA-181 and the other two strains harbored blaOXA-48-like genes, with open reading frame (ORF) similarities with blaOXA-48 ranging from 98.49% to 99.62%. The two novel blaOXA-48-like genes, named blaOXA-1038 and blaOXA-1039, respectively, were cloned and expressed in E. coli. The three OXA-48-like enzymes demonstrated significant hydrolysis activity against meropenem, and the classical β-lactamase inhibitor had no significant inhibitory effect. In conclusion, this study demonstrated the diversity of the blaOXA gene and highlighted the emergence of novel OXA carbapenemases in S. xiamenensis. Further attention to S. xiamenensis and OXA carbapenemases is recommended for the effective prevention and control of antibiotic-resistant bacteria.

Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches.

Carbapenem-resistant Enterobacteriaceae (CRE) are a global threat to human health and are increasingly being isolated from nonclinical settings. OXA-48-producing Escherichia coli sequence type 38 (ST38) is the most frequently reported CRE type in wild birds and has been detected in gulls or storks in North America, Europe, Asia, and Africa. The epidemiology and evolution of CRE in wildlife and human niches, however, remains unclear. We compared wild bird origin E. coli ST38 genome sequences generated by our research group and publicly available genomic data derived from other hosts and environments to (i) understand the frequency of intercontinental dispersal of E. coli ST38 clones isolated from wild birds, (ii) more thoroughly measure the genomic relatedness of carbapenem-resistant isolates from gulls sampled in Turkey and Alaska, USA, using long-read whole-genome sequencing and assess the spatial dissemination of this clone among different hosts, and (iii) determine whether ST38 isolates from humans, environmental water, and wild birds have different core or accessory genomes (e.g., antimicrobial resistance genes, virulence genes, plasmids) which might elucidate bacterial or gene exchange among niches. Our results suggest that E. coli ST38 strains, including those resistant to carbapenems, are exchanged between humans and wild birds, rather than separately maintained populations within each niche. Furthermore, despite close genetic similarity among OXA-48-producing E. coli ST38 clones from gulls in Alaska and Turkey, intercontinental dispersal of ST38 clones among wild birds is uncommon. Interventions to mitigate the dissemination of antimicrobial resistance throughout the environment (e.g., as exemplified by the acquisition of carbapenem resistance by birds) may be warranted. IMPORTANCE Carbapenem-resistant bacteria are a threat to public health globally and have been found in the environment as well as the clinic. Some bacterial clones are associated with carbapenem resistance genes, such as Escherichia coli sequence type 38 (ST38) and the carbapenemase gene blaOXA-48. This is the most frequently reported carbapenem-resistant clone in wild birds, though it was unclear if it circulated within wild bird populations or was exchanged among other niches. The results from this study suggest that E. coli ST38 strains, including those resistant to carbapenems, are frequently exchanged among wild birds, humans, and the environment. Carbapenem-resistant E. coli ST38 clones in wild birds are likely acquired from the local environment and do not constitute an independent dissemination pathway within wild bird populations. Management actions aimed at preventing the environmental dissemination and acquisition of antimicrobial resistance by wild birds may be warranted.

PREVELANCE OF CARBAPENEMASE PRODUCING ORGANISMS AND MOLECULAR RAPID DETECTION OF DIFFERENT GENES FROM VARIOUS CLINICAL ISOLATES IN PATIENTS ADMITTED AT TERTIARY CARE HOSPITALS OF VADODARA

Introduction- Carbapenemase-producing organisms (CPO) have been identied as an urgent healthcare threat. The spread of carbapenemase-producing Enterobacterales (CPE) is a global health problem of great concern. Rapid detection of carbapenemase-producing organisms is clinically desirable for hospital infection control and antibiotic stewardship. Recently, an on-demand polymerase chain reaction (PCR) assay, namely, the Xpert CarbaR assay, that requires less than an hour of turnaround time, had been developed for CPO detection in clinical samples to identify and guide infection control programs to contain the spread of CPO within a hospital. Objective- Carba-R assay is a qualitative multiplex real-time PCR method that qualitatively detects and differentiates ve common carbapenemase genes blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP) directly from clinical samples or puried colonies within approximately 1 hour. This benets hospitals and patients by facilitating timely Infection Prevention &amp; Control measures, thereby reducing risk of exposure, transmission and bed-days lost. Materials &amp; Methods- In this study, the Xpert Carba-R assay was evaluated for detection of the ve carbapenemase genes (blaKPC, blaNDM, blaIMP, blaOXA-48, and blaVIM) in total of 40 non duplicate various clinical samples of admitted patients in tertiary care hospitals of Vadodara. Result- We performed Carba-R on 40 isolates: 18 blood samples, 06 urine, 05 rectal swabs, 03 Endotracheal secretion, 03 Pus, 02 wound discharge, 01 Bronchoalveolar lavage uid, 01 sputum, and 01 ERCP stent isolates. 36/40 (90%) isolates had one or more carbapenemase genes. They were as follows: 19/40 (47.5%) both OXA48 and NDM , 12/40 (30%) NDM and 05/40(12.5%) OXA-48. There were 04/40 (10 %) isolates which were Carbapenem resistant on disc diffusion &amp; VITEK but none of the resistant genes were detected possibly due to other resistant mechanism like efux pump and porin channels. Klebsiella pneumoniae was the most common isolate with CR, 34/40 (85%). The most frequent genes encountered in Klebsiella pneumoniae were both OXA48 and NDM, 19/34 (55.88%), NDM 08/34 (23.53%) followed by OXA 48, 05/34 (14.71%) and Out of 34 Klebsiella isolates, 02 isolates failed to detect any of these ve carbapenemase genes. Conclusion- Xpert Carba-R assay provides good reliable results for detection and differentiation of ve carbapenemase genes in clinical isolates. Compared to bacterial culture followed by PCR identication of resistance genes from colonies, the Carba-R assay reduced turnaround time from 48 to 72 hours to less than 1 hour. Carbapenemase genes were detected by the Carba-R assay in Klebsiella pneumoniae (34/40), Escherichia coli (5/40), Acinetobacter spp (1/40). The Carba-R assay detected 19 both OXA48 and NDM (47.5%), 12 blaNDM (30% and 05 blaOXA-48 (12.5%) genes. Laboratory detection of these genes may help improve patient outcomes by tailoring therapy. This study was conducted for understanding the molecular epidemiology of Carbapenemase producing Enterobacteriaceae in a tertiary care hospital. The combined use of the Xpert Carba-R assay and culture produces rapid and reliable results for the active surveillance of CPO in patients

Nosocomial infections and antimicrobial susceptibility patterns among patients admitted to intensive care unitofImam Khomeinihospitalin Ilam, Iran.

Nosocomial infections (NIs) are a major challenge worldwide. Identification of antibiotic resistance pattern extended spectrum beta-lactamases (ESBLs) and carbapenem-resistant Enterobacteriaceae (CRE) were the objectives of this study. In this cross-sectional study, the antimicrobial susceptibility pattern of bacterial isolates collected from patients with NIs in ICU was determined. Overall, 42 Escherichia coli and Klebsiella pneumoniae isolates from different infection sites were used to determine phenotypic tests of ESBLs, Metallo-β-lactamases (MBLs) and CRE. Detection of ESBLs, MBLs and CRE genes were performed by the polymerase chain reaction (PCR) method. From 71 patients with NIs, 103 different bacterial strains were isolated. The most frequently isolated bacteria were E. coli (n = 29; 28.16%), Acinetobacter baumannii (n = 15; 14.56%), and K. pneumoniae (n = 13; 12.26%). Also, the rate of multidrug-resistant (MDR) isolates was 58.25% (60/103). Based on phenotypic confirmation tests, 32 (76.19%) isolates of E. coli and K. pneumoniae produced ESBLs, and 6 (14.28%) isolates were identified as CRE producers. PCR showed the high prevalence of the blaCTX-M (n = 29; 90.62%) in ESBL genes. In addition, blaNDM was detected in 4 (66.66%), blaOXA-23 in 3 (50%), and blaOXA-48 gene in 1 (16.66%) isolates. The blaVIM, blaKPC, and blaIMP genes were not detected in any of the isolates. The Gram-negative bacteria E. coli, A. baumannii, and K. pneumoniae with high resistance levels were the most common bacteria causing NIs in the ICU. This study for the first time identified blaOXA-11, blaOXA-23, and blaNDM-1 genes in E. coli and K. pneumoniae in Ilam city of Iran.

High prevalence of clonally related ST182 NDM-1-producing Enterobacter cloacae complex clinical isolates in Greece

NDM-type metallo-β-lactamase (MBL)-producing Enterobacterales remain uncommon in the European region, especially among species other than Klebsiella pneumoniae and Escherichia coli. The aim of this study was to describe epidemiological and molecular characteristics of a widespread NDM-1-producing Enterobacter cloacae complex outbreak in Greece. Over a 6-year period (March 2016-March 2022), a retrospective study was conducted in a tertiary care Greek hospital. Ninety single-patient carbapenem-non-susceptible E. cloacae complex clinical isolates were recovered consecutively. The isolates were subjected to further investigation, including antimicrobial susceptibility testing and combined disc tests for carbapenemase production, polymerase chain reaction and sequencing for resistance genes, molecular fingerprinting by pulsed-field gel electrophoresis (PFGE), plasmid profiling, replicon typing, conjugation experiments, genotyping by multi-locus sequence typing (MLST), whole-genome sequencing and phylogenetic analysis. Phenotypic and molecular testing confirmed the presence of blaNDM-1 in 47 (52.2%) of the E. cloacae complex isolates. MLST analysis clustered all but four of the NDM-1 producers into a single MLST sequence type (ST182), whereas single isolates belonged to different sequence types (ST190, ST269, ST443 and ST743). PFGE analysis revealed that ST182 isolates were clustered into a single clonal type, with three subtypes, which differed from the clonal types detected among the remaining carbapenem non-susceptible E. cloacae complex isolates identified during the study period. All ST182 blaNDM-1-carrying isolates also harboured the blaACT-16 AmpC gene, while the blaESBL, blaOXA-1 and blaTEM-1 genes were detected in most cases. In all clonal isolates, the blaNDM-1 gene was located on an IncA/C-type plasmid, and flanked upstream by an ISAba125 element and downstream by bleMBL. Conjugation experiments failed to produce carbapenem-resistant transconjugants, indicating a low dynamic for horizontal gene transfer. Application of enforced infection control measures led to the absence of new NDM-positive cases for periods of time during the survey. This study represents the largest clonal outbreak of NDM-producing E. cloacae complex in Europe.

Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis.

The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance. A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis. The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621. Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.

The First Report of Escherichia coli and Klebsiella pneumoniae Strains That Produce Both NDM-5 and OXA-181 in Jiangsu Province, China.

The aim of this study was to analyze the genetic characteristics of three Enterobacteriaceae strains (one strain of Escherichia coli and two strains of Klebsiella pneumoniae) that produce both the NDM-5 and OXA-181 carbapenemases in pediatric patients. Carbapenem-resistant Enterobacteriaceae (CRE) strains were collected from the Children's Hospital Affiliated to Nanjing Medical University in 2022. Resistance genes were detected by PCR. CRE strains that produced both the blaNDM-5 and blaOXA-181 genes were further characterized by antimicrobial susceptibility testing, multilocus sequence typing (MLST), plasmid conjugation assay, S1 nuclease-PFGE, Southern blotting and whole-genome sequencing. Three Enterobacteriaceae strains carrying both the blaNDM-5 and blaOXA-181 resistance genes were screened. MLST results showed that the strain of Escherichia coli carrying both blaNDM-5 and blaOXA-181 was ST410; the two strains of Klebsiella pneumoniae with both blaNDM-5 and blaOXA-181 were ST2601 and ST759. Conjugation assays showed that the plasmids harboring the blaNDM-5 and blaOXA-181 genes were self-transmissible. S1-PFGE and Southern blotting showed that the blaNDM-5 and blaOXA-181 genes were located on the plasmid with the size of about 60kb~. The genotyping results showed that the plasmid types were ColKP3 and IncX3. This is the first report of Enterobacteriaceae strains that produce both NDM-5 and OXA-181 isolated from pediatric patients in China. Active infection control measures are urgently needed to prevent the spread of bacteria in children.

Study the Role of the Efflux Pump in Multidrug-Resistant Acinetobacter baumannii

Thirty-one A. baumannii isolates were obtained from Shar and Burn hospitals in Sulaimani City, KRG-Iraq. Bacterial identification was confirmed by detecting both 16S rRNA and blaOXA-51 genes. The detection of carbapenem resistant isolates was carried out using Kirby- Bauer, RAPDEC Carba NP and combined disc assays. A high rate of drug resistance was observed, as 74.2% of the isolates were multidrug-resistant (MDR) and 38.7% were extensively drug-resistant (XDR), while carbapenem-resistant A. baumannii (CRAB) comprised approximately 58% of the isolates. Among CRAB isolates, carbapenemase production was detected by using the RAPDEC Carba NP and the combined disc assays in 88.8% (16/18) and 55.5% (10/18) of the isolates respectively. Phenotypic activity of efflux pump was detected among 22.5% of all isolates and 38.8% of CRAB isolates. PCR successfully identified the adeA, adeB, adeC, adeR, and adeS genes in 83.9%, 90.3%, 58%, 80.6%, and 90.3% of the isolates, respectively.&#x0D; Eight mutations in adeR and 15 mutations in adeS regulatory genes were recorded. We conclude that carbapenem resistance mechanisms in A. bumanni isolates included mutations in adeRS regulatory genes and production of carbapenemase.

Virulence, antimicrobial resistance, and molecular characteristics of carbapenem-resistant Klebsiella pneumoniae in a hospital in Shijiazhuang City from China

Carbapenem-resistant Klebsiella pneumoniae (CRKP), as one of the most common drug-resistant bacteria threatening human health, is hyper-resistant to multiple antimicrobial drugs and carbapenems, which can be dealt with only limited clinical treatment options. This study described the epidemiological characteristics of CRKP in this tertiary care hospital from 2016 to 2020. Specimen sources included blood, sputum, alveolar lavage fluid, puncture fluid, secretions from a burn wound, and urine. Among the 87 carbapenem-resistant strains, ST11 was the predominant isolate, followed by ST15, ST273, ST340, and ST626. These STs were in broad agreement with the STs defined by pulsed-field gel electrophoresis clustering analysis in discriminating clusters of related strains. Most CRKP isolates contained the blaKPC-2 gene, some isolates carried the blaOXA-1, blaNDM-1, and blaNDM-5 genes, and the isolates carrying carbapenem resistance genes were more resistant to the antimicrobials of β-lactams, carbapenems, macrolides, and fluoroquinolone. The OmpK35 and OmpK37 genes were detected in all CRKP strains, and the Ompk36 gene was detected in some CRKP strains. All detected OmpK37 had 4 mutant sites, and OmpK36 had 11 mutant sites, while no mutant sites were found in OmpK35. More than half of the CRKP strains contained the OqxA and OqxB efflux pump genes. The virulence genes were most commonly combined with urea-wabG-fimH-entB-ybtS-uge-ycf. Only one CRKP isolate was detected with the K54 podoconjugate serotype. This study elucidated the clinical epidemiological features and molecular typing of CRKP, and grasped the distribution of drug-resistant genotypes, podocyte serotypes, and virulence genes of CRKP, providing some guidance for the subsequent treatment of CRKP infection.

Serotype distribution, trend of multidrug resistance and prevalence of β-lactamase resistance genes in human Salmonella isolates from clinical specimens in Guizhou, China.

Salmonella, one of the major causes of foodborne infections, can cause bacterial foodborne illness. We investigated the serotype distribution, multidrug resistance (MDR), and β-lactamase resistance genes of human Salmonella isolates collected from clinical specimens in Guizhou, China, between 2013 and 2018. A total of 363 Salmonella isolates were collected from clinical specimens at 17 surveillance hospitals. Twenty-four serotypes were identified by sliding agglutination test. S. Enteritidis (33.9%), Salmonella 4,[5],12:i:- (24.0%), S. Typhimurium (16.3%), S. London (6.3%), and S. Derby (3.9%) were the top five serotypes. In 2018, the most common serotype changed from S. Enteritidis to S. Typhimurium. Among the 363 Salmonella isolates, 97.5% of isolates were resistant to at least one class of antimicrobial agents. For cephalosporins, ceftriaxone had the highest resistance rate of 10.5%, and cefepime and cefoxitin were 8.0% and 2.2%, respectively. Three hundred and one (82.9%) Salmonella isolates showed MDR. Salmonella 4,[5],12:i:- had the highest MDR rate with 94.2%, followed by S. London (91.3%) and S. Typhimurium (88.1%). Multidrug resistance rates of Salmonella isolates in Guizhou from 2013 to 2017 increased from 75.8% to 86.7%. Sixteen isolates (4.4%) showed extensive drug resistance. One hundred thirty-four antimicrobial resistance patterns were found. Two hundred and forty-one (66.4%) isolates carried at least one β-lactamase resistance gene. The blaTEM gene (61.2%) was the most prevalent resistant gene in all Salmonella isolates, followed by the blaCTX-M gene (6.1%) and blaOXA-1 gene (4.1%). Our findings showed that the MDR rate of Salmonella isolates from Guizhou province increased year by year. Therefore, systematic and long-term surveillance on MDR Salmonella isolates from clinical patients should be further strengthened.

First Report of OXA-181-Producing Enterobacterales Isolates in Latin America.

We characterized five carbapenemase-producing Enterobacterales (CPE) isolates from two health care institutions in Lima, Peru. The isolates were identified as Klebsiella pneumoniae (n = 3), Citrobacter portucalensis (n = 1), and Escherichia coli (n = 1). All were identified as blaOXA-48-like gene carriers using conventional PCR. Whole-genome sequencing found the presence of the blaOXA-181 gene as the only carbapenemase gene in all isolates. Genes associated with resistance to aminoglycosides, quinolones, amphenicols, fosfomycins, macrolides, tetracyclines, sulfonamides, and trimethoprim were also found. The plasmid incompatibility group IncX3 was identified in all genomes in a truncated Tn6361 transposon flanked by ΔIS26 insertion sequences. The qnrS1 gene was also found downstream of blaOXA-181, conferring fluoroquinolone resistance to all isolates. CPE isolates harboring blaOXA-like genes are an increasing public health problem in health care settings worldwide. The IncX3 plasmid is involved in the worldwide dissemination of blaOXA-181, and its presence in these CPE isolates suggests the wide dissemination of blaOXA-181 in Peru. IMPORTANCE Reports of carbapenemase-producing Enterobacterales (CPE) isolates are increasing worldwide. Accurate detection of the β-lactamase OXA-181 (a variant of OXA-48) is important to initiate therapy and preventive measures in the clinic. OXA-181 has been described in CPE isolates in many countries, often associated with nosocomial outbreaks. However, the circulation of this carbapenemase has yet to be reported in Peru. Here, we report the detection of five multidrug-resistant CPE clinical isolates harboring blaOXA-181 in the IncX3-type plasmid, a potential driver of dissemination in Peru.

Detection of biofilm-related genes and antibiotic resistance in Acinetobacter baumannii isolated from clinical specimens

Abstract. Saadulla SOK, Muhammed SM. 2023. Detection of biofilm-related genes and antibiotic resistance in Acinetobacter baumannii isolated from clinical specimens. Biodiversitas 24: 1809-1816. A total of 53 Acinetobacter baumannii clinical isolates were collected from patients treated at Shar Hospital in Sulaimani city to determine antibiotic susceptibility patterns and their association between biofilm formation and the distribution of biofilm-related genes. Identification of suspected A. baumannii was carried out by conventional and molecular approaches, including 16S rRNA and blaoxa-51 gene amplification. In addition, disk diffusion and microtiter plate methods determined antibiotic susceptibility and biofilm-forming capability, respectively. Out of 53 A. baumannii clinical isolates 42 (79.24%), were Multidrug-Resistant (MDR), of which 3 (5.66%) were resistant to colistin. Overall, 33 (62.26%) of the clinical isolates were strong biofilm producers, 6 (11.32%) were moderate or weak biofilm producers, and 8 (15.09%) were non-biofilm-forming isolates. The frequency of biofilm-related genes ompA, bap, csuE, blaPER-1, and cpaA among A. baumannii strains was 92.45%, 79.24%, 73.58%, 9.43%, and 7.54%, respectively. The high frequency of multi-drug resistant strains, and their ability to form biofilms, is a potential threat to effective therapy and may increase morbidity and mortality in infected patients. Colistin appeared to be the most effective antibiotic for treating MDR A. baumannii infections.

Investigation of antimicrobial resistance patterns and molecular typing of Pseudomonas aeruginosa isolates among Coronavirus disease-19 patients

BackgroundPseudomonas aeruginosa is a common co-infecting pathogen recognized among COVID-19 patients. We aimed to investigate the antimicrobial resistance patterns and molecular typing of Pseudomonas aeruginosa isolates among Coronavirus disease-19 patients.MethodsBetween December 2020 and July 2021, 15 Pseudomonas aeruginosa were isolated from COVID-19 patients in the intensive care unit at Sina Hospital in Hamadan, west of Iran. The antimicrobial resistance of the isolates was determined by disk diffusion and broth microdilution methods. The double-disk synergy method, Modified Hodge test, and polymerase chain reaction were utilized to detect Pseudomonas aeruginosa extended spectrum beta-lactamase and carbapenemase producers. Microtiter plate assay was performed to evaluate the biofilm formation ability of the isolates. The isolates phylogenetic relatedness was revealed using the multilocus variable-number tandem-repeat analysis method.ResultsThe results showed Pseudomonas aeruginosa isolates had the most elevated resistance to imipenem (93.3%), trimethoprim-sulfamethoxazole (93.3%), ceftriaxone (80%), ceftazidime (80%), gentamicin (60%), levofloxacin (60%), ciprofloxacin (60%), and cefepime (60%). In the broth microdilution method, 100%, 100%, 20%, and 13.3% of isolates showed resistance to imipenem, meropenem, polymyxin B, and colistin, respectively. Ten (66.6%) isolates were identified as multiple drug resistance. Carbapenemase enzymes and extended spectrum beta-lactamases were identified in 66.6% and 20% of the isolates, respectively and the biofilm formation was detected in 100% of the isolates. The blaOXA-48, blaTEM, blaIMP, blaSPM, blaPER, blaVEB, blaNDM, blaSHV, and blaCTX-M genes were detected in 100%, 86.6%, 86.6%, 40%, 20%, 20%, 13.3%, 6.6%, and 6.6% of the isolates, respectively. The blaVIM, blaGIM, blaGES, and blaMCR-1 genes were not identified in any of the isolates. The MLVA typing technique showed 11 types and seven main clusters and most isolates belong to cluster I, V and VII.ConclusionDue to the high rate of antimicrobial resistance, as well as the genetic diversity of Pseudomonas aeruginosa isolates from COVID-19 patients, it is indispensable to monitor the antimicrobial resistance pattern and epidemiology of the isolates on a regular basis.

Increased clonal dissemination of OXA-232-producing ST15 Klebsiella pneumoniae in Zhejiang, China from 2018 to 2021

BackgroundOXA-232-producing Klebsiella pneumoniae was first identified in China in 2016, and its clonal transmission was reported in 2019. However, there are no prevalence and genotypic surveillance data available for OXA-232 in China. Therefore, we investigated the trends and characteristics of OXA-232 type carbapenemase in Zhejiang Province, China from 2018 to 2021.MethodsA total of 3278 samples from 1666 patients in the intensive care units were collected from hospitals in Zhejiang Province from 2018 to 2021. Carbapenem-resistant isolates were initially selected by China Blue agar plates supplemented with 0.3 μg/ml meropenem, and further analyzed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry identification, immune colloidal gold technique, conjugation experiment, antimicrobial susceptibility testing and whole genome sequencing.ResultsA total of 79 OXA-producing strains were recovered, with the prevalence increased from 1.8% [95% confidence interval (CI): 0.7–3.7%] in 2018 to 6.0% (95% CI: 4.4–7.9%) in 2021. Seventy-eight strains produced OXA-232 and one produced OXA-181. The blaOXA-232 gene in all strains was located in a 6141-bp ColKP3-type non-conjugative plasmid and the blaOXA-181 gene was located in a 51,391-bp ColKP3/IncX3-type non-conjugative plasmid. The blaOXA-232-producing K. pneumoniae was dominated (75/76) by isolates of sequence type 15 (ST15) that differed by less than 80 SNPs. All OXA-producing strains (100%, 95% CI: 95.4–100.0%) were multidrug-resistant.ConclusionsFrom 2018 to 2021, OXA-232 is the most prevalent OXA-48-like derivative in Zhejiang Province, and ST15 K. pneumoniae isolates belonging to the same clone are the major carriers. The transmission of ColKP3-type plasmid to E. coli highlighted that understanding the transmission mechanism is of great importance to delay or arrest the propagation of OXA-232 to other species.

Identification and Characterization of OXA-232-Producing Sequence Type 231 Multidrug Resistant Klebsiella pneumoniae Strains Causing Bloodstream Infections in China.

Klebsiella pneumoniae, a notorious pathogen for opportunistic health care-associated infections, represents increasing multidrug resistance, particularly to carbapenems. OXA-232 carbapenemase, as a variant of OXA-48, has been increasingly reported worldwide. ST231, an epidemic, multidrug resistant (MDR) K. pneumoniae clone in south and southeast Asia, has been found in other regions, including Europe. In the study, five OXA-232 carbapenemase-producing Klebsiella pneumoniae isolates, four of which belong to sequence type 231 (ST231) and one of which belongs to ST15, were isolated from two hospitals in China. All isolates displayed a MDR phenotype, being susceptible to only polymyxin B and colistin, and the blaOXA-232 gene was located on a ColKP3-type nonconjugative plasmid of 6.1 kb. A phylogenetic analysis of the global ST231 K. pneumoniae isolates (n = 231) suggested that the four ST231 isolates from this study gathered with strains from south Asia (especially India), indicating that the emerging Chinese ST231 clone was more closely related to south Asia isolates and might have spread from south Asia, where ST231 was a successful epidemic clone. Virulence assays suggested that the four ST231 strains were not highly virulent, as they displayed significantly lower virulence potential, compared with a ST23 K1 hypervirulent isolate in a G. mellonella infection and in mouse intraperitoneal infection models, although three ST231 strains harbored a plasmid-borne aerobactin-encoding iuc gene cluster. This is the first report of ST231 K. pneumoniae clinical strains bearing blaOXA-232 in China, and it highlights the emergence of the ST231 clone causing bloodstream infections in a health care setting as well as calls attention to the transmission of this emerging clone in China. IMPORTANCE OXA-232 carbapenemase, being a vital resistance mechanism against carbapenems, has recently been increasingly reported. In China, the identified OXA-232-producing K. pneumoniae isolates almost belonged to ST15 and were not hypervirulent, despite harboring a virulence plasmid. Here, we report the first occurrence in China of a MDR OXA-232-producing K. pneumoniae ST231 clone that is an epidemic ST type in south and southeast Asia. A phylogenetic analysis indicated that this emerging Chinese ST231 clone was more closely related to Indian isolates. The occurrence of this clone may have been driven through the transnational importation of Indian ST231 K. pneumoniae clones. Moreover, this study is the first to assess the virulence potential of ST231 clones that have never been estimated in previous studies. While the high burden of MDR K. pneumoniae is concerning, genomic surveillance can shed light on the transmission chains of novel MDR clones, and active surveillance should be enforced to restrict the spread of MDR isolates.