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152500.8997Genetic Characterization of Enterobacter hormaechei Co-Harboring bla (NDM-1) and mcr-9 Causing Upper Respiratory Tract Infection. PURPOSE: With the spread of multiple drug-resistant bacteria, bla (NDM-1) and mcr-9 have been detected in various bacteria worldwide. However, the simultaneous detection of bla (NDM-1) and mcr-9 in Enterobacter hormaechei has been rarely reported. This study identified an E. hormaechei strain carrying both bla (NDM-1) and mcr-9. We investigated the genetic characteristics of these two resistance genes in detail, elucidating various potential mechanisms by which they may be transmitted. METHODS: Bacterial genomic features and possible origins were assessed by whole-genome sequencing (WGS) with Illumina and PacBio platforms and phylogenetic analysis. Subsequent investigations were performed, including antimicrobial susceptibility testing and multilocus sequence typing (MLST). RESULTS: We isolated an E. hormaechei strain DY1901 carrying both bla (NDM-1) and mcr-9 from the sputum sample. Susceptibility testing showed that the isolate was multidrug-resistant. Multiple antibiotic resistance genes and virulence genes are widely distributed in DY1901. S1-PFGE, Southern blotting, and plasmid replicon typing showed that DY1901 carried four plasmids. The plasmid carrying mcr-9 was 259Kb in size and belonged to IncHI2, while the plasmid carrying bla (NDM-1) was 45Kb in length and belonged to IncX3. CONCLUSION: The E. hormaechei strain isolated in this study has a broad antibiotic resistance spectrum, posing a challenge to clinical treatment. Plasmids carrying mcr-9 are fusion plasmids, and those taking NDM are widely disseminated in China, suggesting that we should conduct routine genomic surveillance on such plasmids to curb the spread of drug-resistant bacteria in the region.202236068833
153610.8989Complete Genetic Analysis of Plasmids Carried by Two Nonclonal bla(NDM-5)- and mcr-1-Bearing Escherichia coli Strains: Insight into Plasmid Transmission among Foodborne Bacteria. Our objective was to characterize the genetic features of plasmids harbored by two genetically related, MCR-1 and NDM-5-producing Escherichia coli strains recovered from a chicken meat sample. The genetic profiles of all plasmids harbored by the two test strains, namely, 1106 and 1107, were determined by whole-genome sequencing, S1-pulsed-field gel electrophoresis (PFGE), Southern hybridization, and bioinformatics analysis. The transferability of plasmids harbored by the two strains was assessed by filter mating assay. Strains 1106 and 1107 were resistant to almost all the antibiotics, including colistin and fosfomycin, but remained susceptible to amikacin and tigecycline. The plasmids of p1107-NDM-5 and p1106-NDM-5 both contain a class I integron which lacks the ISAba125 element. The backbone of p1106-IncFII exhibited a high degree of similarity with that of p1106-NDM-5 and p1107-NDM-5, implying that events of plasmid fusion and resolution were involved in the formation of the two plasmids. The plasmids p1106-IncHI2MCR and p1107-IncHI2MCR belong to an IncHI2 replicon type, with three copies of ISApl1 being observed in p1106-IncHI2MCR, implying that the mcr-1 gene was transferable among bacteria that reside in the same food matrix. In this study, p1106-IncFIB, p1107-99K, p1107-111K, and p1107-118K were all found to be phage-like plasmids, with p1106-IncFIB and p1107-118K containing several virulence genes, including iroBCDEN, iucABCD, sitABCD, hlyF, and iss. Surprisingly, resistance genes such as aph(3')-Ia, sul3, and aac(3')-IId could also be found in p1107-118K, but resistance genes were not detected in other phage-like plasmids. In conclusion, enhanced surveillance is required to monitor and control the dissemination of various resistance determinants among foodborne pathogens. IMPORTANCE Carbapenem and colistin are last-resort antibiotics used to treat serious clinical infections caused by multidrug-resistant (MDR) bacterial pathogens. Plasmids encoding resistance to carbapenems and colistin have been reported in clinical pathogens in recent years, and yet few studies reported cocarriage of mcr and bla(NDM) genes in Escherichia coli strains of food origin. How plasmids encoding these two important resistance determinants are being evolved and transmitted in bacterial pathogens is not well understood. In this study, we investigated the genetic features of plasmids harbored by two nonclonal, mcr-1- and bla(NDM-5)-bearing E. coli strains (1106 and 1107) recovered from a fresh chicken meat sample to understand and provide evidence of the level and dynamics of MDR plasmid transmission. Our data confirmed that active plasmid fusion and resolution events were involved in the formation of plasmids that harbor multiple resistance genes, which provide insights into the further control of plasmid evolution in bacterial pathogens.202134468190
153120.8979Emergence of Plasmids Co-Harboring Carbapenem Resistance Genes and tmexCD2-toprJ2 in Sequence Type 11 Carbapenem Resistant Klebsiella pneumoniae Strains. OBJECTIVES: To characterize two plasmids co-harboring carbapenem resistance genes and tmexCD2-toprJ2 in carbapenem-resistant Klebsiella pneumoniae (CRKP) strains. METHODS: Two clinical CRKP strains were isolated and characterized by antimicrobial susceptibility testing, conjugation assays, whole-genome sequencing, and bioinformatics analysis. RESULTS: The two CRKP strains NB4 and NB5 were both resistant to imipenem, meropenem and tigecycline. Whole-genome sequencing revealed that two CRKP strains belonged to the ST11 type and carried multiple resistance genes. The tmexCD2-toprJ2 clusters in both strains were located on the IncFIB(Mar)-like/HI1B-like group of hybrid plasmids, which co-harbored the metallo-β-lactamase gene bla(NDM-1). In addition, the co-existence of bla(NDM-1) and bla(KPC-2) and the presence of tmexCD2-toprJ2 in CRKP strain NB5 was observed. CONCLUSIONS: In this study, tmexCD2-toprJ2 gene clusters were identified in two NDM-1-producing CRKP ST11 strains. These gene clusters will likely spread into clinical high-risk CRKP clones and exacerbate the antimicrobial resistance crisis. In addition, we detected the co-occurrence of bla(NDM-1), bla(KPC-2) and tmexCD2-toprJ2 in a single strain, which will undoubtedly accelerate the formation of a "superdrug resistant" bacteria. Hence, effective control measures should be implemented to prevent the further dissemination of such organisms in clinical settings.202235646740
198930.8979Prevalence and characterization of IncQ1α-mediated multi-drug resistance in Proteus mirabilis Isolated from pigs in Kunming, Yunnan, China. BACKGROUND: Proteus mirabilis is a conditionally pathogenic bacterium that is inherently resistant to polymyxin and tigecycline, largely due to antibiotic resistance genes (ARGs). These ARGs can be horizontally transferred to other bacteria, raising concerns about the Inc plasmid-mediated ARG transmission from Proteus mirabilis, which poses a serious public health threat. This study aims to investigate the presence of Inc plasmid types in pig-derived Proteus mirabilis in Kunming, Yunnan, China. METHODS: Fecal samples were collected from pig farms across six districts of Kunming (Luquan, Jinning, Yiliang, Anning, Songming, and Xundian) from 2022 to 2023. Proteus mirabilis isolates were identified using IDS and 16S rRNA gene sequencing. Then, positive strains underwent antimicrobial susceptibility testing and incompatibility plasmid typing. Multi-drug-resistant isolates with positive incompatibility plasmid genes were selected for whole-genome sequencing. Resistance and Inc group data were then isolated and compared with 126 complete genome sequences from public databases. Whole-genome multi-locus sequence typing, resistance group analysis, genomic island prediction, and plasmid structural gene analysis were performed. RESULTS: A total of 30 isolates were obtained from 230 samples, yielding a prevalence of 13.04%. All isolates exhibited multi-drug resistance, with 100% resistance to cotrimoxazole, erythromycin, penicillin G, chloramphenicol, ampicillin, and streptomycin. Among these, 15 isolates tested positive for the IncQ1α plasmid repC gene. The two most multi-drug-resistant and repC-positive strains, NO. 15 and 21, were sequenced to compare genomic features on Inc groups and ARGs with public data. Genome analysis revealed that the repC gene was primarily associated with IncQ1α, with structural genes from other F-type plasmids (TraV, TraU, TraN, TraL, TraK, TraI, TraH, TraG, TraF, TraE/GumN, and TraA) also present. Strain NO. 15 carried 33 ARGs, and strain NO. 21 carried 38 ARGs, conferring resistance to tetracyclines, fluoroquinolones, aminoglycosides, sulfonamides, peptides, chloramphenicol, cephalosporins, lincomycins, macrolides, and 2-aminopyrimidines. CONCLUSION: The repC gene is primarily associated with IncQ1α, with structural genes from other F-type plasmids. A comparison with 126 public genome datasets confirmed this association.202439850143
152840.8977First Report of Coexistence of bla (SFO-1) and bla (NDM-1) β-Lactamase Genes as Well as Colistin Resistance Gene mcr-9 in a Transferrable Plasmid of a Clinical Isolate of Enterobacter hormaechei. Many antimicrobial resistance genes usually located on transferable plasmids are responsible for multiple antimicrobial resistance among multidrug-resistant (MDR) Gram-negative bacteria. The aim of this study is to characterize a carbapenemase-producing Enterobacter hormaechei 1575 isolate from the blood sample in a tertiary hospital in Wuhan, Hubei Province, China. Antimicrobial susceptibility test showed that 1575 was an MDR isolate. The whole genome sequencing (WGS) and comparative genomics were used to deeply analyze the molecular information of the 1575 and to explore the location and structure of antibiotic resistance genes. The three key resistance genes (bla (SFO-1), bla (NDM-1), and mcr-9) were verified by PCR, and the amplicons were subsequently sequenced. Moreover, the conjugation assay was also performed to determine the transferability of those resistance genes. Plasmid files were determined by the S1 nuclease pulsed-field gel electrophoresis (S1-PFGE). WGS revealed that p1575-1 plasmid was a conjugative plasmid that possessed the rare coexistence of bla (SFO-1), bla (NDM-1), and mcr-9 genes and complete conjugative systems. And p1575-1 belonged to the plasmid incompatibility group IncHI2 and multilocus sequence typing ST102. Meanwhile, the pMLST type of p1575-1 was IncHI2-ST1. Conjugation assay proved that the MDR p1575-1 plasmid could be transferred to other recipients. S1-PFGE confirmed the location of plasmid with molecular weight of 342,447 bp. All these three resistant genes were flanked by various mobile elements, indicating that the bla (SFO-1), bla (NDM-1), and mcr-9 could be transferred not only by the p1575-1 plasmid but also by these mobile elements. Taken together, we report for the first time the coexistence of bla (SFO-1), bla (NDM-1), and mcr-9 on a transferable plasmid in a MDR clinical isolate E. hormaechei, which indicates the possibility of horizontal transfer of antibiotic resistance genes.202134220761
519350.8976Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia. BACKGROUND: Stenotrophomonas maltophilia (S. maltophilia) is the first dominant ubiquitous bacterial species identified from the genus Stenotrophomonas in 1943 from a human source. S. maltophilia clinical strains are resistance to several therapies, this study is designed to investigate the whole genome sequence and antimicrobial resistance genes prediction in Stenotrophomonas maltophilia (S. maltophilia) SARC-5 and SARC-6 strains, isolated from the nasopharyngeal samples of an immunocompromised patient. METHODS: These bacterial strains were obtained from Pakistan Institute of Medical Sciences (PIMS) Hospital, Pakistan. The bacterial genome was sequenced using a whole-genome shotgun via a commercial service that used an NGS (Next Generation Sequencing) technology called as Illumina Hiseq 2000 system for genomic sequencing. Moreover, detailed in-silico analyses were done to predict the presence of antibiotic resistance genes in S. maltophilia. RESULTS: Results showed that S. maltophilia is a rare gram negative, rod-shaped, non sporulating bacteria. The genome assembly results in 24 contigs (>500 bp) having a size of 4668,850 bp with 65.8% GC contents. Phylogenetic analysis showed that SARC-5 and SARC-6 were closely related to S. maltophilia B111, S. maltophilia BAB-5317, S. maltophilia AHL, S. maltophilia BAB-5307, S. maltophilia RD-AZPVI_04, S. maltophilia JFZ2, S. maltophilia RD_MAAMIB_06 and lastly with S. maltophilia sp ROi7. Moreover, the whole genome sequence analysis of both SARC-5 and SARC-6 revealed the presence of four resistance genes adeF, qacG, adeF, and smeR. CONCLUSION: Our study confirmed that S. maltophilia SARC-5 and SARC-6 are one of the leading causes of nosocomial infection which carry multiple antibiotic resistance genes.202438128408
519260.8976Genome Sequencing Analysis of a Rare Case of Blood Infection Caused by Flavonifractor plautii. BACKGROUND Flavonifractor plautii belongs to the clostridium family, which can lead to local infections as well as the bloodstream infections. Flavonifractor plautii caused infection is rarely few in the clinic. To understand better Flavonifractor plautii, we investigated the drug sensitivity and perform genome sequencing of Flavonifractor plautii isolated from blood samples in China and explored the drug resistance and pathogenic mechanism of the bacteria. CASE REPORT The Epsilometer test method was used to detect the sensitivity of flavonoid bacteria to antimicrobial agents. PacBio sequencing technology was employed to sequence the whole genome of Flavonifractor plautii, and gene prediction and functional annotation were also analyzed. Flavonifractor plautii displayed sensitivity to most drugs but resistance to fluoroquinolones and tetracycline, potentially mediated by tet (W/N/W). The total genome size of Flavonifractor plautii was 4,573,303 bp, and the GC content was 59.78%. Genome prediction identified 4,506 open reading frames, including 9 ribosomal RNAs and 66 transfer RNAs. It was detected that the main virulence factor-coding genes of the bacteria were the capsule, polar flagella and FbpABC, which may be associated with bacterial movement, adhesion, and biofilm formation. CONCLUSIONS The results of whole-genome sequencing could provide relevant information about the drug resistance mechanism and pathogenic mechanism of bacteria and offer a basis for clinical diagnosis and treatment.202438881048
172170.8973Convergence of MCR-8.2 and Chromosome-Mediated Resistance to Colistin and Tigecycline in an NDM-5-Producing ST656 Klebsiella pneumoniae Isolate From a Lung Transplant Patient in China. We characterized the first NDM-5 and MCR-8.2 co-harboring ST656 Klebsiella pneumoniae clinical isolate, combining with chromosomal gene-mediated resistance to colistin and tigecycline. The K. pneumoniae KP32558 was isolated from the bronchoalveolar lavage fluid from a lung transplant patient. Complete genome sequences were obtained through Illumina HiSeq sequencing and nanopore sequencing. The acquired resistance genes and mutations in chromosome-encoded genes associated with colistin and tigecycline resistance were analyzed. Comparative genomic analysis was conducted between mcr-8.2-carrying plasmids. The K. pneumoniae KP32558 was identified as a pan-drug resistant bacteria, belonging to ST656, and harbored plasmid-encoded bla(NDM-5) and mcr-8.2 genes. The bla(NDM-5) gene was located on an IncX3 type plasmid. The mcr-8.2 gene was located on a conjugative plasmid pKP32558-2-mcr8, which had a common ancestor with another two mcr-8.2-carrying plasmids pMCR8_020135 and pMCR8_095845. The MIC of KP32558 for colistin was 256 mg/L. The mcr-8.2 gene and mutations in the two-component system, pmrA and crrB, and the regulator mgrB, had a synergistic effect on the high-level colistin resistance. The truncation in the acrR gene, related to tigecycline resistance, was also identified. K. pneumoniae has evolved a variety of complex resistance mechanisms to the last-resort antimicrobials, close surveillance is urgently needed to monitor the prevalence of this clone.202235899054
540780.8970Resistance mechanisms and tedizolid susceptibility in clinical isolates of linezolid-resistant bacteria in Japan. OBJECTIVES: Studies combining linezolid resistance mechanisms and tedizolid susceptibility in linezolid-resistant clinical isolates are scarce. This study investigated the linezolid resistance mechanisms and tedizolid susceptibility of linezolid-resistant strains isolated clinically in Japan. METHODS: We analysed 25 linezolid-resistant strains of Enterococcus faecium and Enterococcus faecalis isolated from Japanese hospitals between 2015 and 2021. MICs of linezolid and tedizolid were determined using the agar plate dilution method. Each 23S rRNA copy was amplified by PCR, sequenced and analysed for mutations. The linezolid resistance genes cfr, poxtA, optrA, fexA and fexB were also detected by PCR. RESULTS: Drug susceptibility tests revealed that five linezolid-resistant E. faecium isolates had low (≤1 mg/L) tedizolid MICs. Resistance mechanisms included the G2576T mutation in 23S rRNA, the T2504A mutation and the resistance genes optrA, fexA and fexB. The T2504A mutation was identified in one E. faecium isolate, which exhibited linezolid and tedizolid MICs of 64 and 32 mg/L, respectively. CONCLUSIONS: Some linezolid-resistant isolates demonstrated low (≤1 mg/L) tedizolid MICs. To determine whether tedizolid susceptibility testing should be performed on linezolid-resistant isolates, more linezolid-resistant isolates should be collected and tested for tedizolid MICs. Tedizolid MICs were 2-3 doubling dilutions lower than linezolid MICs. The results of this study suggest that future research should investigate whether the T2504A mutation contributes to tedizolid resistance. To our knowledge, this is the first study to report tedizolid susceptibility in E. faecium with the T2504A mutation and in isolate harbouring this mutation.202540463587
149390.8965Coexistence of blaKPC-2 and blaNDM-1 in one IncHI5 plasmid confers transferable carbapenem resistance from a clinical isolate of Klebsiella michiganensis in China. OBJECTIVES: This study firstly identified an IncHI5 plasmid pK254-KPC_NDM co-carrying two different class carbapenemase genes blaKPC-2 and blaNDM-1 in Klebsiella michiganensis K254. METHODS: The strain K254 was sequenced by high-throughput genome sequencing. A detailed genomic and phenotypic characterization of pK254-KPC_NDM was performed. RESULTS: pK254-KPC_NDM displayed the conserve IncHI5 backbone and carried a resistant accessory region: Tn1696-related transposon Tn7414 containing blaKPC-2 and blaNDM-1. A sequence comparison was applied to a collection of four Tn1696-related transposons (Tn7414-Tn7417) harbouring carbapenemase genes. For all these four transposons, the blaNDM-1 was carried by Tn125 derivatives within three different mobile genetic elements. Tn7414 further acquired another carbapenemase gene, blaKPC-2, because of the integration of the local blaKPC-2 genetic environment from Tn6296, resulting in the high-level carbapenem resistance of K. michiganensis K254. The conjugal transfer and plasmid stability experiments confirmed that pK254-KPC_NDM could be transferred intercellularly and keep the stable vertical inheritance in different bacteria, which would contribute to the further dissemination of multiple carbapenemase genes and enhance the adaption and survival of K. michiganensis under complex and diverse antimicrobial selection pressures. CONCLUSION: This study was the first to report the K. michiganensis isolate coharbouring blaKPC-2 and blaNDM-1 in the Tn1696-related transposon in IncHI5 plasmid. The emergence of novel transposons simultaneously carrying multiple carbapenemase genes might contribute to the further dissemination of high-level carbapenem resistance in the isolates of the hospital settings and pose new challenges for the treatment of nosocomial infection.202337714378
5211100.8965Pediococcus pentosaceus IMI 507025 genome sequencing data. The genome sequence data for the pickled cucumbers isolate, Pediococcus pentosaceus IMI 507025, is reported. The raw reads and analysed genome reads were deposited at NCBI under Bioproject with the accession number PRJNA814992. The number of contigs before and after trimming were 17 and 12 contigs, respectively. The total size of the genome was 1,795,439 bp containing 1,811 total genes, of which 1,751 were coding sequences. IMI 507025 identity was determined via average nucleotide identity (ANI), obtaining an identity value of 99.5994% between IMI 507025 and the type strain P. pentosaceus ATCC 33316, identifying the strain as P. pentosaceus. Screening for the antimicrobial resistance (AMR) and virulence genes in the genome of IMI 507025 showed no hits, confirming the safety of the tested strain. Presence of plasmids was not found.202235864877
1390110.8965Oxacillinase-484-Producing Enterobacterales, France, 2018-2023. We examined the emergence and characteristics of oxacillinase-484-producing Enterobacterales in France during 2012-2023. Genomic analysis identified 2 predominant sequence types in Escherichia coli: ST410 and ST1722. Plasmid analysis revealed that bla(OXA-484) genes were carried mostly on an IncX3-type plasmid associated with genetic elements including insertion sequences IS3000 and ISKpn19.202439320334
5205120.8963Antimicrobial resistance and virulence factors of Klebsiella quasipneumoniae, the novel sequence types (ST) 7979 and 7980 from Indonesia. Klebsiella pneumoniae is a human pathogen of global concern. The more recently described pathogen, K. quasipneumoniae, shares similar morphological characteristics with K. pneumoniae and is commonly misidentified as this species using conventional laboratory techniques. This study investigates the molecular characteristics of four phenotype-identified K. pneumoniae isolates obtained from hospital wastewater in Jakarta, Indonesia. Whole-genome sequencing (WGS) and the Average Nucleotide Identity (ANI) showed that these isolates were eventually identified as K. quasipneumoniae subsp. quasipneumoniae, a closely related species of K. pneumoniae. These isolates of novel ST7979 and ST7980 strains are classified as multi-drug resistant (MDR) bacteria and harbor many antibiotic-resistance genes. Interestingly, the novel ST7980 strain is carbapenem non-susceptible and harbors the sul1 gene and the heat-stable enterotoxin gene, astA. The ST7979 strains have KL55 capsular type and O3b type, whereas the ST7980 strains have KL107 and O12 types. Our finding highlights the significance of identifying the K. quasipneumoniae strain utilizing a genomic platform. Additionally, routine surveillance is needed to monitor the hospital wastewater and avoid the spread of multidrug-resistant bacteria.202540609771
1519130.8963Epidemiology and resistance mechanisms of tigecycline- and carbapenem-resistant Enterobacteriaceae in China: a multicentre genome-based study. OBJECTIVES: To elucidate the molecular epidemiology of tigecycline and carbapenem-resistant Enterobacteriaceae isolates and mechanisms of tigecycline resistance. METHODS: We gathered 31 unduplicated strains of tigecycline-resistant Enterobacteriaceae from six hospitals nationwide. Antimicrobial susceptibility testing, phenotypic detection, and PCR identification were performed first, followed by homology analysis using MLST and PFGE. Conjugation transfer experiments using resistance gene plasmids were carried out, and the conjugates' growth curves were examined. All strains were sequenced using the Illumina HiSeq technology, and we identified a strain KP28 carrying a complete gene cluster tmexCD2-toprJ2. Then, its plasmid was further constructed using the PacBio platforms to complete the frame. The genetic connection of the tmexCD2-toprJ2 gene cluster carried by KP28 was established using core genome analyses. RESULTS: All 31 tigecycline-resistant Enterobacteriaceae strains (TG-CRE) were multidrug resistant. PFGE classified strains of CRKP, CRECL, and CRKAE into 16 distinct spectra, 6 distinct spectra, and 3 distinct spectra. MLST results showed a high concentration of ST11 in CRKP strains and a predominance of ST116 in CRECL strains, suggesting possible clonal transmission or selective dominance. The findings of the plasmid conjugation assay revealed that three strains expressing carbapenem resistance genes were effectively transmitted to the recipient cell E. coli EC600. WGS data revealed that these 31 strains include 79 resistance genes, with one strain (KP28) carrying the whole tigecycline resistance gene cluster, tmexC2D2-toprJ2. This resistance gene is contained in a large IncHI5 plasmid, which is difficult to transfer. CONCLUSION: The overall carriage rate of the tmexC2D2-toprJ2 gene cluster was found to be low among the five Chinese hospitals investigated. Conversely, tet(A) mutations were present in most of the strains. Bacteria with the carbapenem resistance genes bla (KPC) and bla (NDM) are vulnerable to horizontal transmission. Increasing the risk of transmission of antibiotic-resistant genes.202540400686
5206140.8962Draft genome sequence of an extensively drug-resistant Pseudomonas aeruginosa isolate belonging to ST644 isolated from a footpad infection in a Magellanic penguin (Spheniscus magellanicus). OBJECTIVES: The incidence of multidrug-resistant bacteria in wildlife animals has been investigated to improve our knowledge of the spread of clinically relevant antimicrobial resistance genes. The aim of this study was to report the first draft genome sequence of an extensively drug-resistant (XDR) Pseudomonas aeruginosa ST644 isolate recovered from a Magellanic penguin with a footpad infection (bumblefoot) undergoing rehabilitation process. METHODS: The genome was sequenced on an Illumina NextSeq(®) platform using 150-bp paired-end reads. De novo genome assembly was performed using Velvet v.1.2.10, and the whole genome sequence was evaluated using bioinformatics approaches from the Center of Genomic Epidemiology, whereas an in-house method (mapping of raw whole genome sequence reads) was used to identify chromosomal point mutations. RESULTS: The genome size was calculated at 6436450bp, with 6357 protein-coding sequences and the presence of genes conferring resistance to aminoglycosides, β-lactams, phenicols, sulphonamides, tetracyclines, quinolones and fosfomycin; in addition, mutations in the genes gyrA (Thr83Ile), parC (Ser87Leu), phoQ (Arg61His) and pmrB (Tyr345His), conferring resistance to quinolones and polymyxins, respectively, were confirmed. CONCLUSION: This draft genome sequence can provide useful information for comparative genomic analysis regarding the dissemination of clinically significant antibiotic resistance genes and XDR bacterial species at the human-animal interface.201829277728
1517150.8962Co-occurrence of blaNDM-1, rmtC, and mcr-9 in multidrug-resistant Enterobacter kobei strain isolated from an infant with urinary tract infection. OBJECTIVES: The co-emergence of mcr and carbapenem resistance genes in Gram-negative bacteria is a serious problem. This study aims to clarify the genetic characteristic of one novel multidrug-resistant Enterobacter kobei EC1382 with mcr-9 causing urinary tract inflammation in an infant. METHODS: Antimicrobial drug susceptibility testing was performed for this isolate using the broth microdilution method. Whole-genome sequencing was performed using the Illumina PacBio RS II platform and HiSeq platform, and the antimicrobial resistance genes, mobile elements, and plasmid replicon types were identified. Conjugation analysis was performed using Escherichia coli C600 as recipients. RESULTS: Enterobacter kobei EC1382 was resistant to carbapenem, aminoglycoside, and cephalosporin. Twenty-five antimicrobial resistance genes were identified, including genes conferring resistance to carbapenem (blaNDM-1), colistin (mcr-9), and aminoglycosides (rmtC). The blaNDM-1 gene, accompanied by bleMBL and rmtC located downstream of an ISCR14 element, was detected in the IncFII(Yp) type plasmid pEC1382-2. Interestingly, although E. kobei EC1382 was susceptible to colistin, it had three identical mcr-9 genes (two in the chromosome and one in the IncHI2-type plasmid pEC1382-1). The backbone (∼12.2-kb genetic fragment) of these mcr-9 (flanked by IS903B and IS481-IS26) regions were conserved in this strain, and they were found to be present in various bacteria as three types, implying a silent distribution. CONCLUSIONS: To the best of our knowledge, this is the first study to demonstrate the coexistence of blaNDM-1, rmtC, and mcr-9 in E. kobei. The silent prevalence of mcr-9 in bacteria may be a threat to public health.202337062506
5203160.8960Draft genome sequence analysis of a novel MLST (ST5028) and multidrug-resistant Klebsiella quasipneumoniae subsp. similipneumoniae (Kp4) strain 456S1 isolated from a pig farm in China. OBJECTIVES: The avian breeding industry is an important element in exposing bacteria to antibiotics. As one of the major animal welfare and economic problems for the poultry industry, multidrug-resistant Klebsiella spp. have become a substantial source of antibiotic resistance genes. In the present work, we reported the draft genome sequence of a novel multilocus sequence type (MLST) (ST5028) Klebsiella quasipneumoniae subsp. similipneumoniae (Kp4) strain 456S1, which was isolated from a pig farm in China with broad-spectrum antimicrobial activities. METHODS: Classical microbiological methods were applied to isolate and identify the strain, genomic DNA was sequenced using an Illumina HiSeq platform, and the reads were de novo assembled into contigs using CLC Genomics Workbench. The assembled contigs were annotated, and whole-genome sequencing (WGS) analysis was performed. RESULTS: WGS analysis revealed that the genome of strain 456S1 comprised a circular chromosome of 5,419,059 bp (GC content, 57.8%), harbouring 12 important antibiotic resistance genes: aac(6')-ib-cr, aadA16, floR, dfrA27, fosA, tet(D), blaOKP-B-3, oqxA, oqxB, qnrB6, sul1 and arr-3. The Klebsiella quasipneumoniae subsp. similipneumoniae (Kp4) 456S1 was also found to belong to a novel sequence type (ST5028) determined by MLST. CONCLUSION: The genome sequence reported herein will provide useful information for antibiotic resistance and pathogenic mechanisms in Klebsiella quasipneumoniae and will be a reference for comparative analysis with genomic features among different sources of clinically important multidrug-resistant strains, especially among bacteria of animal and human origin.202133516893
958170.8958Whole-Genome Analysis of Multidrug-Resistant Klebsiella pneumoniae Kp04 Reveals Distinctive Antimicrobial and Arsenic-Resistance Genomic Features: A Case Study from Bangladesh. Multidrug-resistant bacteria, particularly extended-spectrum-beta-lactamase-producing (ESBL) bacteria, pose a significant global public health challenge. Klebsiella pneumoniae (KPN) is frequently implicated in cases of this resistance. This study aimed to investigate the presence of drug and metal resistance genes in clinical K. pneumoniae isolate Kp04 and comparative genomics of clinical KPN isolates characterized from Bangladesh. A total of 12 isolates were collected. Disk-diffusion assay showed that all five isolates were resistant to 14 out of 21 tested antibiotics and sensitive to only three-tigecycline, imipenem, and meropenem. KPN Kp04 was positive for both bla(SHV) and bla(CTX-M) ESBL genes in PCR. All five isolates produced PCR amplicons of the correct size for ampicillin (ampC), tetracycline (tetC), fluoroquinolone (qnrS), and aminoglycoside (aadA) resistance genes. The whole genome of Kp04 was sequenced using the MiSeq Platform (V3 kit, 2 × 300 cycles). We utilized different databases to detect Antibiotic-Resistant Genes (ARGs), virulence factor genes (VFGs), and genomic functional features of the Kp04 strain. Whole-genome sequencing identified 75 ESBL, virulence, and multiple drug-resistant (MDR) genes including bla(SHV), tetA, oqxA, oqxB, aadA, sul1-5, and mphA in KPN Kp04 isolate. Pan-genomic analysis of 43 Bangladeshi KPN isolates showed similarities between Dhaka and Chattogram isolates regarding virulence and antibiotic-resistant genes. Our results indicate the transmission of similar virulent KPN strains in Dhaka and Chattogram. This study would provide valuable information about drug sensitivity, antibiotic, and metal resistance features of K. pneumoniae circulated among hospitalized patients in Bangladeshi megacities.202439613891
2107180.8958Virulence, 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.202337097488
2993190.8957Antibiotic resistant zoonotic bacteria in Irrawaddy squirrel (Callosciurus pygerythrus). Irrawaddy squirrel (Callosciurus pygerythrus) may play an important role in the transmission of zoonotic bacteria, but little is known about the carriage of zoonotic bacteria in this common frugivorous rodent in Bangladesh. We aimed to investigate the presence of common zoonotic bacterial pathogens in Irrawaddy squirrel in the southeast part of Bangladesh. A total of 27 rectal and 27 oro-nasal swabs were collected from 27 healthy wild Irrawaddy squirrels. Four common zoonotic bacteria were isolated following routine laboratory procedures, and were identified based on colony morphology, and biochemical and staining properties. The pathogenic potential of the identified bacteria was confirmed by detection of virulence genes by PCR. All isolates were subjected to antimicrobial susceptibility test against seven antibiotics from six generic groups which are commonly used in human and veterinary medicine in Bangladesh. The prevalence of Escherichia coli, Salmonella spp., Yersinia spp. and Staphylococcus spp. was 44.4% (95% CI, 32.0-57.6), 13% (95% CI, 6.1-24.7), 44.4% (95% CI, 32.0-57.6), and 72.2% (95% CI, 59.0-82.5), respectively. We identified potential zoonotic virulence genes in all of these four bacterial species. Antimicrobial susceptibility testing revealed the presence of several multidrug resistant bacterial strains in squirrels. To the best of our knowledge, this is the first report in Bangladesh of the detection of antibiotic resistant zoonotic bacteria in Irrawaddy squirrels. The findings underpin the role of Irrawaddy squirrel as a source of pathogenic antibiotic resistant bacteria, consequently, fruit rejected because of squirrel consumption and squirrel-bites deserve more concern than previously.201930488592