Determination of a novel integron-located variant (bla OXA -320 ) of Class D β-lactamase in Proteus mirabilis

From Turkey: First Report of KPC-3- and CTX-M-27-Producing Multidrug-Resistant Klebsiella pneumoniae ST147 Clone Carrying OmpK36 and Ompk37 Porin Mutations

Aim: The aim of this study was to identify antimicrobial resistance genes, virulence factor genes, and porin loss or mutations exhibited by the multidrug-resistant Klebsiella pneumoniae strain. Materials and Methods: Whole-genome sequencing was done via the Illumina NovaSeq 6000 platform. Strain identification and antibiotic susceptibility testing of strains were performed by the Vitek 2 automated system. Multilocus sequence typing analysis was carried out using seven conserved housekeeping genes. Results: The strain was resistant to penicillins, cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, fosfomycin, and trimethoprim/sulfamethoxazole. The isolate was found to carry KPC-3, CTX-M-27, SHV-11, SHV-67, and TEM-1 β-lactamases. The clonal subtype of the isolate was ST147, and it possessed wzi64 and wzc38 alleles. Fifteen different point mutations (N49S, L59V, R146H, V178P, G189T, F198Y, V202L, F207Y, A217S, T222L, D223G, H235N, A280V, N304E, and S346N) were detected in the OmpK36 porin. A frame shift was observed in OmpK35 and two different point mutations (I70M and I128M) were found in the OmpK37 porin, in addition to seven mutations observed on the AcrR. Conclusions: This study demonstrated for the first time that the ST147 clone produced CTX-M-27 as well as KPC-3. In addition, new mutations were detected in the outer membrane proteins. These mutations together with the production of extended-spectrum β-lactamase and carbapenemase were found to contribute to the resistance of the ST147 clone to carbapenem and other antibiotics.

Antimicrobial Resistance Caused by KPC-2 Encoded by Promiscuous Plasmids of the Klebsiella pneumoniae ST307 Strain

Background

A lineage of Klebsiella pneumoniae that produces carbapenemase-2 (KPC-2), sequence type (ST) 307, emerged in 2017. We analyzed the complete sequences of plasmids from KPC-2-producing K. pneumoniae (KPC-Kp) ST307, investigated the antimicrobial resistance conferred by this strain, and confirmed the horizontal interspecies transmission of KPC-carbapenemase-producing Enterobacteriaceae (CPE) characteristics among Enterobacteriaceae.

Methods

We performed antimicrobial susceptibility testing, PCR analysis, multilocus sequence typing, curing tests, and whole-genome sequencing to characterize plasmid-derived KPC-2-producing Enterobacteriaceae clinical isolates.

Results

Sequence analysis of KPC-Kp strain ST307 revealed novel plasmid-located virulence factors, including a gene cluster for glycogen synthesis. Three Enterobacteriaceae strains were identified in one patient: K. pneumoniae (CPKp1825), Klebsiella aerogenes (CPEa1826), and Escherichia coli (CPEc1827). The bla_KPC-2 gene from K. pneumoniae ST307 was horizontally transmitted between these strains. The plasmids could be transferred through conjugation, because all three strains of bacteria contained the type IV secretion system, pilus genes, and tra genes for conjugal transfer. The bla_KPC-2 gene was located on a truncated Tn4401 transposon. Plasmids containing the bla_KPC-2 gene could not be artificially removed; thus, the three strains could not be cured.

Conclusions

The ease of horizontal transfer of KPC-Kp ST307 carbapenem resistance has serious public health and epidemiological implications. This study provides a better understanding of the genetic characteristics that can contribute to the growth and spread of KPC-Kp ST307, and their association with antimicrobial resistance genes.

Species Transferability of Klebsiella pneumoniae Carbapenemase-2 Isolated from a High-Risk Clone of Escherichia coli ST410

Sequence type 410 (ST410) of Escherichia coli is an extraintestinal pathogen associated with multi drug resistance. In this study, we aimed to investigate the horizontal propagation pathway of a highrisk clone of E. coli ST410 that produces Klebsiella pneumoniae carbapenemase (KPC). blaKPCencoding E. coli and K. pneumoniae isolates were evaluated, and complete sequencing and comparative analysis of blaKPC-encoding plasmids from E. coli and K. pneumoniae, antimicrobial susceptibility tests, polymerase chain reaction, multilocus sequence typing, and conjugal transfer of plasmids were performed. Whole-genome sequencing was performed for plasmids mediating KPC-2 production in E. coli and K. pneumoniae clinical isolates. Strains E. coli CPEc171209 and K. pneumoniae CPKp171210 were identified as ST410 and ST307, respectively. CPEc171209 harbored five plasmids belonging to serotype O8:H21, which is in the antimicrobial-resistant clade C4/H24. The CPKp171210 isolate harbored three plasmids. Both strains harbored various additional antimicrobial resistance genes. The IncX3 plasmid pECBHS_9_5 harbored blaKPC-2 within a truncated Tn4401a transposon, which also contains blaSHV-182 with duplicated conjugative elements. This plasmid displayed 100% identity with the IncX3 plasmid pKPBHS_10_3 from the K. pneumoniae CPKp171210 ST307 strain. The genes responsible for the conjugal transfer of the IncX3 plasmid included tra/trb clusters and pil genes coding the type IV pilus. ST410 can be transmitted between patients, posing an elevated risk in clinical settings. The emergence of a KPC-producing E. coli strain (ST410) is concerning because the blaKPC-2-bearing plasmids may carry treatment resistance across species barriers. Transgenic translocation occurs among carbapenem-resistant bacteria, which may spread rapidly via horizontal migration.

Genetics of Acquired Antibiotic Resistance Genes in Proteus spp

Proteus spp. are commensal Enterobacterales of the human digestive tract. At the same time, P. mirabilis is commonly involved in urinary tract infections (UTI). P. mirabilis is naturally resistant to several antibiotics including colistin and shows reduced susceptibility to imipenem. However higher levels of resistance to imipenem commonly occur in P. mirabilis isolates consecutively to the loss of porins, reduced expression of penicillin binding proteins (PBPs) PBP1a, PBP2, or acquisition of several antibiotic resistance genes, including carbapenemase genes. In addition, resistance to non-β-lactams is also frequently reported including molecules used for treating UTI infections (e.g., fluoroquinolones, nitrofurans). Emergence and spread of multidrug resistant P. mirabilis isolates, including those producing ESBLs, AmpC cephalosporinases and carbapenemases, are being more and more frequently reported. This review covers Proteus spp. with a focus on the different genetic mechanisms involved in the acquisition of resistance genes to multiple antibiotic classes turning P. mirabilis into a dreadful pandrug resistant bacteria and resulting in difficult to treat infections.

First report of blaOXA-24 carbapenemase gene, armA methyltransferase and aac(6')-Ib-cr among multidrug-resistant clinical isolates of Proteus mirabilis in Algeria

OBJECTIVE

Carbapenemase-producing, or carbapenem-resistant, Enterobacteriaceae are an emerging threat to human and animal health because they are resistant to many of the last-line antimicrobials available for treatment of infection. The aim of this study was to analyse the antimicrobial resistance patterns and their encoding genes of Proteus mirabilis isolated in Constantine, Algeria.

METHODS

A total of 108 Proteus, Morganella and Providencia (PMP) strains were isolated from a large variety of clinical specimens at University Hospital of Constantine in Algeria. Isolates were identified using the API 20E system and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Diagnostic accuracy was determined by independent comparison of each method to phylogenetic analysis based on 16S rRNA gene sequencing. Antimicrobial susceptibility was determined by the standard disk diffusion and Etest methods. The presence of antimicrobial resistance genes was screened for by PCR amplification and sequencing.

RESULTS

A total of 72 PMP strains were multidrug-resistant (MDR). Among them, one P. mirabilis isolate was resistant to imipenem with a minimum inhibitory concentration (MIC) of ≥12μg/mL. PCR and sequencing showed the presence of various antimicrobial resistance genes, including bla_CTX-M-15, bla_TEM-1, bla_TEM-2, bla_PER-1, bla_SHV-11, aadA1, aadA2, armA, aac(6')-Ib, aac(6')-Ib-cr, aac(3)-Ia and ant(2″)-I, forming different resistance profiles. Moreover, the bla_OXA-24 gene was detected in the imipenem-resistant P. mirabilis strain.

CONCLUSION

In this study, a MDR P. mirabilis isolate harbouring the bla_OXA-24, armA 16S rRNA methylase and aac(6)-Ib-cr genes was found for the first time in Algeria.

Distribution of β-lactamase genes among carbapenem-resistant Klebsiella pneumoniae strains isolated from patients in Turkey

Background

The emergence of carbapenem-resistant Klebsiella pneumoniae poses a serious problem to antibiotic management. We investigated the β-lactamases in a group of carbapenem-resistant K. pneumoniae clinical isolates from Turkey.

Methods

Thirty-seven strains of K. pneumoniae isolated from various clinical specimens were analyzed by antimicrobial susceptibility testing, PCR for the detection of β-lactamase genes, DNA sequencing, and repetitive extragenic palindronic (REP)-PCR analysis.

Results

All 37 isolates were resistant to ampicillin, ampicillin/sulbactam, piperacillin, piperacillin/tazobactam, ceftazidime, cefoperazone/sulbactam, cefepime, imipenem, and meropenem. The lowest resistance rates were observed for colistin (2.7%), tigecycline (11%), and amikacin (19%). According to PCR and sequencing results, 98% (36/37) of strains carried at least one carbapenemase gene, with 32 (86%) carrying OXA-48 and 7 (19%) carrying NDM-1. No other carbapenemase genes were identified. All strains carried a CTX-M-2-like β-lactamase, and some carried SHV- (97%), TEM- (9%), and CTX-M-1-like (62%) β-lactamases. Sequence analysis of bla_TEM genes identified a bla_TEM-166 with an amino acid change at position 53 (Arg53Gly) from bla_TEM-1b, the first report of a mutation in this region. REP-PCR analysis revealed that there were seven different clonal groups, and temporo-spatial links were identified within these groups.

Conclusions

Combinations of β-lactamases were found in all strains, with the most common being OXA-48, SHV, TEM, and CTX-M-type (76% of strains). We have reported, for the first time, a high prevalence of the NDM-1 (19%) carbapenemase in carbapenem-resistant K. pneumoniae from Turkey. These enzymes often co-exist with other β-lactamases, such as TEM, SHV, and CTX-M β-lactamases.