Molecular characterization of beta-lactamase genes and their genetic structures in Acinetobacter genospecies 3 isolates in Taiwan

Phenotypic and genotypic characterization of clinical carbapenem-resistant Acinetobacter species harboring the metallo-beta-lactamases IMP-8 or NDM-1 in China

Carbapenem-resistant Acinetobacter spp. pose a significant challenge in clinical settings due to limited treatment options for nosocomial infections. Carbapenem-hydrolyzing class D beta-lactamases are the primary cause for carbapenem resistance, while metallo-beta-lactamases (MBLs) New Delhi metallo beta-lactamase (NDM) and imipenemase (IMP) also contribute. This study investigated five MBL-producing Acinetobacter spp. strains isolated from a clinic in China in 2010. The blaIMP-8-carrying A1014 was the first identified CRAB among all known STPas150 isolates worldwide. Through whole-genome sequencing and the southern blot analysis, we determined that blaIMP-8 was located on a pR4WN-type plasmid and blaNDM-1 was located on four distinct pSU1904NDM-type plasmids. The blaIMP-8 gene was identified within a class 1 integron organized as a 5'-conserved segment (intI), variable region (blaIMP-8-aac(6')-Ib), and 3'-conserved segment (qacEΔ1/sul1). All available sequences of blaIMP variants in A. baumannii from the NCBI were investigated and classified into five types of class 1 integrons. All blaNDM-1 plasmids were transferable, and the blaNDM-1 genes were in a conservative region. Additionally, multiple resistance genes, including those conferring resistance to aminoglycosides, tetracyclines, and macrolides, were detected on plasmids from these strains. All strains were resistant to meropenem and imipenem, while they were all susceptible to tigecycline and intermediate to polymyxin. A207 and A1014 were susceptible to cefiderocol, and only blaIMP-8-carrying A1014 had low MIC value (4/2 µg/mL) toward cefoperazone/sulbactam. In conclusion, we characterized the phenotypic and genotypic features of one IMP-8-producing and four NDM-1-producing plasmids recovered from Acinetobacter spp. strains isolated in 2010, contributing to the understanding of the dissemination and evolution of these enzymes.

IMPORTANCE

Given the low prevalence of IMP among A. baumannii and the limited sequencing technology in earlier years, research on blaIMP in A. baumannii is scarce, and genetic information on blaNDM-1-producing Acinetobacter spp. strains isolated in earlier years is limited. This study revisited five MBL-carrying Acinetobacter spp. strains isolated in 2010, characterizing their phenotypic and genotypic features. This retrospective analysis serves as a form of "bacterial archaeology," providing evidence of the evolutionary changes in genetic elements conferring antibiotic resistance.

Acinetobacter Non-baumannii Species: Occurrence in Infections in Hospitalized Patients, Identification, and Antibiotic Resistance

BACKGROUND

Acinetobacter species other than A. baumannii are becoming increasingly more important as opportunistic pathogens for humans. The primary aim of this study was to assess the prevalence, species distribution, antimicrobial resistance patterns, and carbapenemase gene content of clinical Acinetobacter non-baumannii (Anb) isolates that were collected as part of a sentinel surveillance program of bacterial infections in hospitalized patients. The secondary aim was to evaluate the performance of MALDI-TOF MS systems for the species-level identification of Anb isolates.

METHODS

Clinical bacterial isolates were collected from multiple sites across Russia and Kazakhstan in 2016-2022. Species identification was performed by means of MALDI-TOF MS, with the Autobio and Bruker systems used in parallel. The PCR detection of the species-specific blaOXA-51-like gene was used as a means of differentiating A. baumannii from Anb species, and the partial sequencing of the rpoB gene was used as a reference method for Anb species identification. The susceptibility of isolates to antibiotics (amikacin, cefepime, ciprofloxacin, colistin, gentamicin, imipenem, meropenem, sulbactam, tigecycline, tobramycin, and trimethoprim-sulfamethoxazole) was determined using the broth microdilution method. The presence of the most common in Acinetobacter-acquired carbapenemase genes (blaOXA-23-like, blaOXA-24/40-like, blaOXA-58-like, blaNDM, blaIMP, and blaVIM) was assessed using real-time PCR.

RESULTS

In total, 234 isolates were identified as belonging to 14 Anb species. These comprised 6.2% of Acinetobacter spp. and 0.7% of all bacterial isolates from the observations. Among the Anb species, the most abundant were A. pittii (42.7%), A. nosocomialis (13.7%), the A. calcoaceticus/oleivorans group (9.0%), A. bereziniae (7.7%), and A. geminorum (6.0%). Notably, two environmental species, A. oleivorans and A. courvalinii, were found for the first time in the clinical samples of patients with urinary tract infections. The prevalence of resistance to different antibiotics in Anb species varied from <4% (meropenem and colistin) to 11.2% (gentamicin). Most isolates were susceptible to all antibiotics; however, sporadic isolates of A. bereziniae, A. johnsonii, A. nosocomialis, A. oleivorans, A. pittii, and A. ursingii were resistant to carbapenems. A. bereziniae was more frequently resistant to sulbactam, aminoglycosides, trimethoprim-sulfamethoxazole, and tigecycline than the other species. Four (1.7%) isolates of A. bereziniae, A. johnsonii, A. pittii were found to carry carbapenemase genes (blaOXA-58-like and blaNDM, either alone or in combination). The overall accuracy rates of the species-level identification of Anb isolates with the Autobio and Bruker systems were 80.8% and 88.5%, with misidentifications occurring in 5 and 3 species, respectively.

CONCLUSIONS

This study provides important new insights into the methods of identification, occurrence, species distribution, and antibiotic resistance traits of clinical Anb isolates.

Characterization of a bla NDM-1-Bearing IncHI5-Like Plasmid From Klebsiella pneumoniae of Infant Origin

The spread of plasmid-mediated carbapenem-resistant clinical isolates is a serious threat to global health. In this study, an emerging NDM-encoding IncHI5-like plasmid from Klebsiella pneumoniae of infant patient origin was characterized, and the plasmid was compared to the available IncHI5-like plasmids to better understand the genetic composition and evolution of this emerging plasmid. Clinical isolate C39 was identified as K. pneumoniae and belonged to the ST37 and KL15 serotype. Whole genome sequencing (WGS) and analysis revealed that it harbored two plasmids, one of which was a large IncHI5-like plasmid pC39-334kb encoding a wide variety of antimicrobial resistance genes clustered in a single multidrug resistance (MDR) region. The bla_NDM-1 gene was located on a ΔISAba125-bla_NDM-1-ble_MBL-trpF-dsbC structure. Comparative genomic analysis showed that it shared a similar backbone with four IncHI5-like plasmids and the IncHI5 plasmid pNDM-1-EC12, and these six plasmids differed from typical IncHI5 plasmids. The replication genes of IncHI5-like plasmids shared 97.06% (repHI5B) and 97.99% (repFIB-like) nucleotide identity with those of IncHI5 plasmids. Given that pNDM-1-EC12 and all IncHI5-like plasmids are closely related genetically, the occurrence of IncHI5-like plasmid is likely associated with the mutation of the replication genes of pNDM-1-EC12-like IncHI5 plasmids. All available IncHI5-like plasmids harbored 262 core genes encoding replication and maintenance functions and carried distinct MDR regions. Furthermore, 80% of them (4/5) were found in K. pneumoniae from Chinese nosocomial settings. To conclude, this study expands our knowledge of the evolution history of IncHI5-like plasmids, and more attention should be paid to track the evolution pathway of them among clinical, animal, and environmental settings.

NDM-1-producing Acinetobacter baumannii ST85 now in Turkey, including one isolate from a Syrian refugee

New Delhi metallo-β-lactamase-1 (NDM-1), an acquired class B carbapenemase, is a significant clinical threat owing to the extended hydrolysis of β-lactams including carbapenems. Here, to the best of our knowledge we describe for the first time in Turkey two NDM-1-producing Acinetobacter baumannii isolates recovered from intensive care unit patients. The presence of blaNDM-1 was detected by PCR and confirmed by sequencing. The clonal relationship was assessed by PFGE and multilocus sequence typing. Both isolates were positive for blaNDM-1 and were attributed with the sequence type 85. One isolate was from a Syrian refugee, whereas the second was from a patient who had never travelled outside Turkey. Our findings confirmed that the rapid spread of NDM-1-producing Gram-negative organisms could become a major challenge for the treatment and control of healthcare-associated infections in our geographical area. They suggest also that NDM-1-producing strains and/or their genetic determinants are probably being imported from Syria to neighbouring countries.

Molecular epidemiology of carbapenem non-susceptible Acinetobacter nosocomialis in a medical center in Taiwan

The mechanism by which carbapenem non-susceptible Acinetobacter nosocomialis (CNSAN) is disseminated is rarely described in the literature. In this study, we delineated the molecular epidemiology of CNSAN isolated from patients in a medical center in Taiwan. Fifty-four non-duplicate bloodstream isolates of CNSAN were collected at the Taipei Veterans General Hospital between 2001 and 2007. Pulsed-field gel electrophoresis (PFGE) was performed to determine their clonal relationship. Carbapenem-resistance genes and associated genetic structures were detected by polymerase chain reaction (PCR) mapping. Southern hybridization was performed to determine the plasmid location of carbapenem-resistance genes. Transmissibility of these genes to Acinetobacterbaumannii was demonstrated by conjugation tests. The overall carbapenem non-susceptibility rate among A. nosocomialis isolates during the study period was 21.6% (54/250). PFGE revealed three major pulsotypes: H (n=23), I (n=10), and K (n=8). The most common carbapenem-resistance gene was blaOXA-58 (43/54, 79.6%), containing an upstream insertion sequence IS1006 and a truncated ISAba3 (IS1006-ΔISAba3-like-blaOXA-58). All isolates belonging to the pulsotypes H, I, and K carried plasmid located IS1006-ΔISAba3-like-blaOXA-58. A common plasmid carrying ISAba1-blaOXA-82 was found in six isolates, which belonged to five pulsotypes. A type 1 integron that carried blaIMP-1 was detected in different plasmids of seven isolates, which belonged to five pulsotypes. Plasmids carrying these carbapenem-resistant determinants were transmissible from A. nosocomialis to A. baumannii via conjugation. In this medical center, CNSAN mainly emerged through clonal dissemination; propagation of plasmids and integrons carrying carbapenem-resistant determinants played a minor role. This study showed that plasmids carrying carbapenem-resistant determinants are transmissible from A. nosocomialis to A. baumannii.

Modifying enzymes related aminoglycoside: analyses of resistant Acinetobacter isolates

Enzymatic modification of aminoglycosides by nucleotidyltransferases, acetyltransferases and/or phosphotransferases accounts for the majority of aminoglycoside-resistant Acinetobacter isolates. In this study, we investigated the relationship between aminoglycoside resistance and the presence of aminoglycoside-modifying enzymes in Acinetobacter baumannii clinical isolate groups with different resistance profiles. Thirty-two clinical A. baumannii isolates were included in this study. Acinetobacter isolates were divided into 4 groups according to results of susceptibility testing. The presence of genes encoding the following aminoglycoside-modifying enzymes; aph (3')-V1, aph (3')-Ia, aac (3)-Ia, aac (3) IIa, aac (6')-Ih, aac (6')-Ib and ant (2')-Ia responsible for resistance was investigated by PCR in all strains. The acetyltransferase (aac (6')-Ib, aac (3)-Ia) and phosphotransferase (aph (3')-Ia) gene regions were identified in the first group, which comprised nine imipenem, meropenem, and gentamicin-resistant isolates. The acetyltransferase (aac (6')-Ib, aac (3)-Ia), phosphotransferase (aph (3')-VI) and nucleotidyltransferase (ant2-Ia) gene regions were identified in the second group, which was composed of nine imipenem-resistant, meropenem-resistant and gentamicin-sensitive isolates. The acetyltransferase (aac (3)-Ia) and phosphotransferase (aph (3')-Ia) regions were identified in the fourth group, which comprised eight imipenem-sensitive, meropenem-sensitive and gentamicin-resistant isolates. Modifying enzyme gene regions were not detected in the third group, which was composed of six imipenem, meropenem and gentamicin-sensitive isolates. Our data are consistent with previous reports, with the exception of four isolates. Both acetyltransferases and phosphotransferases were widespread in A. baumannii clinical isolates in our study. However, the presence of the enzyme alone is insufficient to explain the resistance rates. Therefore, the association between the development of resistance and the presence of the enzyme and other components should be investigated further.

A case of IMP-4-, OXA-421-, OXA-96-, and CARB-2-producing Acinetobacter pittii sequence type 119 in Australia

An IMP-4-producing Acinetobacter pittii strain coproducing oxacillinases was isolated from a leg wound of a 67-year-old female patient. Identification to the species level by rpoB and gyrB sequencing and multiplex-PCR-based analysis revealed that the isolate was A. pittii. Whole-genome sequencing of this A. pittii isolate determined the presence of blaOXA-96, blaCARB-2, and a novel blaOXA-421 gene. The position of this novel blaOXA-421 gene was similar to that of blaOXA-51 in A. baumannii, downstream of the phosphinothricin N-acetyltransferase gene and upstream of fxsA in the chromosome. This A. pittii isolate was found to belong to sequence type 119 (ST119). Here, we report the first isolation of IMP-4-producing A. pittii ST119 with a novel blaOXA-421 gene from a patient in Australia and characterize its draft genome.

Characterization and plasmid elimination of NDM-1-producing Acinetobacter calcoaceticus from China

The presence of multidrug-resistant bacterial pathogens in the environment poses a serious threat to public health. The opportunistic Acinetobacter spp. are among the most prevalent causes of nosocomial infections. Here, we performed complete genome sequencing of the Acinetobacter calcoaceticus strain XM1570, which was originally cultivated from the sputum of a patient diagnosed with pneumonia in Xiamen in 2010. We identified carbapenem resistance associated gene bla_NDM-1 located on a 47.3-kb plasmid. Three methods – natural reproduction, sodium dodecyl sulfate treatment and nalidixic acid treatment – were used to eliminate the bla_NDM-1-encoding plasmid, which achieved elimination rates of 3.32% (10/301), 83.78% (278/332), and 84.17% (298/354), respectively. Plasmid elimination dramatically increased antibiotic sensitivity, reducing the minimum bacteriostatic concentration of meropenem from 256 µg/ml in the clinical strain to 0.125 µg/ml in the plasmid-eliminated strain. Conjugation transfer assays showed that the bla_NDM-1-containing plasmid could be transferred into Escherichia coli DH5α:pBR322 in vitro as well as in vivo in mice. The bla_NDM-1 genetic environment was in accordance with that of other bla_NDM-1 genes identified from India, Japan, and Hong-Kong. The multilocus sequence type of the isolate was identified as ST-70. Two novel genes encoding intrinsic OXA and ADC were identified and named as OXA-417 and ADC-72. The finding of bla_NDM-1 in species like A. calcoaceticus demonstrates the wide spread of this gene in gram-negative bacteria which is possible by conjugative plasmid transfer. The results of this study may help in the development of a treatment strategy for controlling NDM-1 bacterial infection and transmission.

KPC-2-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan

OBJECTIVES

Two plasmids carrying bla(KPC-2) isolated from carbapenem-resistant Escherichia coli (CR-EC) and carbapenem-resistant Klebsiella pneumoniae (CR-KP), respectively, were completely sequenced. The CR-KP strain was selected from an outbreak in 2012, and the CR-EC strain was the first blaKPC-2-carrying E. coli identified in the same carbapenem resistance monitoring programme in Taiwan.

METHODS

Antimicrobial susceptibility tests, multilocus sequence typing (MLST) and the conjugal transfer of plasmids were performed. Complete sequencing of the plasmids was performed using a shotgun approach.

RESULTS

The CR-EC and CR-KP strains in this study were determined to be ST410 and ST11, respectively, by MLST. From CR-EC, we identified a 145 kb conjugative plasmid that carries bla(KPC-2), bla(CMY-2), bla(CTX-M-3) and bla(TEM-1). The plasmid is a chimera composed of three regions related to IncI, IncN and RepFIC replicons. From CR-KP, we identified an 86.5 kb plasmid, pKPC-LK30, which carries bla(KPC-2) and bla(SHV-11). The plasmid is very similar to two bla(KPC-2)-carrying IncFII(K) plasmids, but lacks one of the replication origins and cannot conjugate.

CONCLUSIONS

The differences in cross-species transferability of the two plasmids can be explained by genetic differences between their backbones and could have resulted in the confined bla(KPC-2)-carrying CR-KP outbreak in Taiwan. Plasmid pKPC-LKEc is the first bla(KPC-2)-carrying plasmid identified from CR-EC in Taiwan. With relatively high transferability it should be closely monitored.

The Acinetobacter baumannii Oxymoron: Commensal Hospital Dweller Turned Pan-Drug-Resistant Menace

During the past few decades Acinetobacter baumannii has evolved from being a commensal dweller of health-care facilities to constitute one of the most annoying pathogens responsible for hospitalary outbreaks and it is currently considered one of the most important nosocomial pathogens. In a prevalence study of infections in intensive care units conducted among 75 countries of the five continents, this microorganism was found to be the fifth most common pathogen. Two main features contribute to the success of A. baumannii: (i) A. baumannii exhibits an outstanding ability to accumulate a great variety of resistance mechanisms acquired by different mechanisms, either mutations or acquisition of genetic elements such as plasmids, integrons, transposons, or resistant islands, making this microorganism multi- or pan-drug-resistant and (ii) The ability to survive in the environment during prolonged periods of time which, combined with its innate resistance to desiccation and disinfectants, makes A. baumannii almost impossible to eradicate from the clinical setting. In addition, its ability to produce biofilm greatly contributes to both persistence and resistance. In this review, the pathogenesis of the infections caused by this microorganism as well as the molecular bases of antibacterial resistance and clinical aspects such as treatment and potential future therapeutic strategies are discussed in depth.

Acinetobacter: a potential reservoir and dispenser for β-lactamases

Innate resistance and remarkable ability to acquire additional resistance determinants underline the clinical importance of Acinetobacter. Over 210 β-lactamases belonging to 16 families have been identified in the genus, mostly in clinical isolates of A. baumannii. In this review, we update the current taxonomy of the genus Acinetobacter and summarize the β-lactamases detected in Acinetobacter spp. with an emphasis on Acinetobacter-derived cephalosporinases (ADCs) and carbapenem-hydrolysing class D β-lactamases (CHDLs). We also discuss the roles of integrons and insertion sequence (IS) elements in the expression and dissemination of such resistance determinants.

Characteristics of carbapenem-resistant Acinetobacter spp. other than Acinetobacter baumannii in South Korea

Although many studies have been performed on carbapenem-resistant Acinetobacter baumannii, only a few studies have addressed carbapenem resistance in Acinetobacter spp. other than A. baumannii (non-baumannii Acinetobacter). Amongst 287 Acinetobacter spp. isolates from patients with bacteraemia in a South Korean hospital collected between 2003 and 2010, 160 (55.7%) were non-baumannii Acinetobacter spp. Antimicrobial susceptibility testing was performed and the effect of efflux pump inhibitors was examined. Antimicrobial resistance genes were identified and pulsed-field gel electrophoresis (PFGE) analysis was performed. OprD expression was also evaluated by quantitative real-time polymerase chain reaction (qRT-PCR), and CarO disruption was investigated by PCR. Seventeen non-baumannii Acinetobacter isolates (10.6%) were resistant to imipenem or meropenem, comprising eight Acinetobacter pittii (or Acinetobacter genomospecies 3), four Acinetobacter nosocomialis (or Acinetobacter genomospecies 13TU), two Acinetobacter genomospecies 'close to 13TU', two Acinetobacter bereziniae (or Acinetobacter genomospecies 10) and one Acinetobacter genomospecies 16. bla(IMP-1) genes were detected in seven and two carbapenem-resistant A. pittii and A. bereziniae isolates, respectively. PFGE showed that A. pittii isolates carrying bla(IMP-1) belonged to the same clone. In addition, bla(SIM-1) and bla(PER-1) genes were simultaneously identified in two A. nosocomialis isolates. In four isolates (one each of A. pittii, A. nosocomialis, Acinetobacter genomospecies 'close to 13TU' and Acinetobacter genomospecies 16), efflux pumps were implicated in the increase in carbapenem minimum inhibitory concentrations. No decreased expression of OprD was identified in any carbapenem-resistant non-baumannii Acinetobacter isolates, and disruption of carO was also not detected. Clonal spread of carbapenem-resistant A. pittii carrying bla(IMP-1), which contributes to a high resistance rate in this species, was identified. The bla(IMP-1) and bla(SIM-1) genes were first identified in A. bereziniae and A. nosocomialis, respectively. Since no carbapenem resistance mechanisms could be identified, further efforts to find the resistance mechanism should be made.

Clinical impact and molecular basis of antimicrobial resistance in non-baumannii Acinetobacter

Species of Acinetobacter other than Acinetobacter baumannii are involved in nosocomial infections. Acinetobacter lwoffii, Acinetobacter genomospecies 3 and Acinetobacter genomospecies 13TU are found in community- and nosocomial-acquired infections as well as in neonatal intensive care units. The non-baumannii Acinetobacter are normally highly susceptible to ciprofloxacin, ampicillin/sulbactam, gentamicin and tigecycline. Carbepenems show good activity although resistant isolates have been reported. Resistance to β-lactams other than carbapenems is associated with overexpression of chromosomal cephalosporinases and extended-spectrum β-lactamase acquisition, whereas resistance to carbapenems involves acquisition of carbapenemases. Quinolone resistance is related to gyrA and/or parC mutations but overexpresion of efflux proteins also plays an important role. With the development of novel and more accurate typing methodologies, an increase in infections caused by non-baumannii Acinetobacter might be observed in the future.

Interspecies dissemination of a novel class 1 integron carrying blaIMP-19 among Acinetobacter species in Japan

OBJECTIVES

To analyse the dissemination of metallo-β-lactamase genes and mobile genetic elements among Acinetobacter spp.

METHODS

From January 2004 to December 2010, 16 Acinetobacter isolates that were positive for metallo-β-lactamase production were collected and analysed. Antimicrobial susceptibilities were studied, and molecular typing was performed using PFGE and multilocus sequence typing (MLST). The resistance genes, including carbapenemase-encoding genes and aminoglycoside resistance genes, were detected by PCR. Mobile genetic elements were identified by nucleotide sequence analysis and PCR mapping of the integron gene cassettes and the insertion sequence (IS) elements.

RESULTS

We identified 10 Acinetobacter genospecies 3 isolates that belonged to three PFGE clusters and four MLST types, 4 Acinetobacter johnsonii isolates that belonged to the same PFGE cluster, 1 Acinetobacter baumannii isolate and 1 Acinetobacter junii isolate. Each isolate was not susceptible to at least one carbapenem. The bla(IMP-19) gene was found in two PFGE clusters of genospecies 3, in the one PFGE cluster of A. johnsonii and in each of the A. baumannii and A. junii isolates, and was located in a class 1 integron as a gene cassette array of bla(IMP-19)-aac(6')-31-bla(OXA-21)-aadA1. One genospecies 3 isolate harboured bla(IMP-11), bla(OXA-58). This isolate harboured three mobile elements, including a class 1 integron that carried bla(IMP-11), another class 1 integron that carried catB8-like/aacA4-aadA5 and an IS element (bla(OXA-58) flanked an either side by ISAba3).

CONCLUSIONS

We demonstrated that the bla(IMP-19) gene carried in the novel class 1 integron gene cassette array of bla(IMP-19)-aac(6')-31-bla(OXA-21)-aadA1 has been horizontally disseminated among different Acinetobacter spp. Additionally, one isolate harboured multiple mobile genetic elements.