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ABSTRACT: Objectives: The emergence of the florfenicol resistance gene fexA in Campylobacter poses a serious threat to public health, but the extent of the spread of fexA in Campylobacter from various hosts has not been well understood. This study aimed to investigate the fexA in Campylobacter isolates from different hosts. Methods: PCR was used to identify fexA-positive Campylobacter from different hosts during 2008–2019 in China, and the fexA-positive isolates were characterized by susceptibility tests, whole-genome sequencing, and natural transformation. Results: A total of 69 (2.54%, 69/2721) fexA-positive Campylobacter were identified, and the fexA-positive isolates increased remarkably (0.42%–16.90%) since it was first detected in 2010. By source, the 69 isolates were obtained from chickens (3.57%, 57/1595), geese (3.43%, 7/204), ducks (1.02%, 2/197), and environments (2.86%, 3/105); the fexA-positive isolates were not isolated in humans and pigs. In addition to fexA, these isolates also carried other antimicrobial resistance genes and exhibited multidrug resistance. Whole-genome sequencing analysis showed the fexA gene can disseminate clonally or horizontally via either multidrug resistance genomic islands or insertion sequences among the Campylobacter. The genetic structure IS1216-∆ISEfa11-hp-fexA-NAD(P)H-∆ISEfa11-IS1216 was conserved and widespread in the Campylobacter of various origins, and the IS1216 can form fexA-carrying circular intermediates, emphasizing that IS1216 plays an important role in the spread of fexA in Campylobacter. Conclusions: This study indicates the wide spread of fexA-positive Campylobacter in poultry and environments. Because multidrug resistance genomic islands and IS1216 can facilitate the transmission of fexA, systematic surveillance should be implemented to prevent the spread of fexA to humans.

The coal-measure source rock in the Chinese sea area plays a significant role as a hydrocarbon source rock, with its genetic environment, development and distribution, and hydrocarbon generation potential serving as essential factors for the exploration of coal-type oil and gas fields. This study focuses on the coal-measure source rock of the Paleogene Enping Formation in the Zhu I Depression, located in the northern South China Sea. The main geological insights obtained are as follows. The coal measures of the Enping Formation are developed in a warm and wet tropical-subtropical climate. The development environment of the coal-measure source rock in the Enping Formation includes the braided river delta upper plain peat swamp, characterized by dry forest swamp coal facies with relatively thick coal seams and a small number of layers. The braided river delta lower plain swamp-interdistributary bay of braided river delta front represents a forest edge-wetland herbaceous swamp coal facies with numerous layers of thin coal seams and poor stability. The shore swamp corresponds to an open water swamp coal facies with multiple layers of thin coal seams and poor stability. The organic matter abundance in the braided river delta upper plain is the highest, followed by the braided river delta lower plain-braided river delta front, and the shore-shallow lake. The organic matter type is predominantly type II1. Thermal evolution analysis suggests that the organic matter has progressed into a substantial oil generation stage. The hydrocarbon generation potential of the coal-measure source rock in the Enping Formation is the highest in the braided river delta upper plain, followed by the braided river delta lower plain-braided river delta front and the shore-shallow lake. Overall, this study proposes three organic facies in the coal-measure source rock of the Enping Formation: upper-plain swamp-dry forest swamp facies, lower plain-interdistributary bay-forest-herbaceous swamp facies, and lake swamp-herbaceous swamp facies. [ABSTRACT FROM AUTHOR]

ABSTRACT OXA-232 carbapenemase is becoming a threat in China due to its high prevalence, mortality, and limited treatment options. However, little information is available on the impact of OXA-232-producing Klebsiella pneumoniae in China. This study aims to characterize the clonal relationships, the genetic mechanisms of resistance, and the virulence of OXA-232-producing K. pneumoniae isolates in China. We collected 81 OXA-232-producing K. pneumoniae clinical isolates from 2017 to 2021. Antimicrobial susceptibility testing was performed using the broth microdilution method. Capsular types, multilocus sequence types, virulence genes, antimicrobial resistance (AMR) determinants, plasmid replicon types, and single-nucleotide polymorphism (SNP) phylogeny were inferred from whole-genome sequences. OXA-232-producing K. pneumoniae strains were resistant to most antimicrobial agents. These isolates showed partial differences in susceptibility to carbapenems: all strains were resistant to ertapenem, while the resistance rates to imipenem and meropenem were 67.9% and 97.5%, respectively. Sequencing and capsular diversity analysis of the 81 K. pneumoniae isolates revealed 3 sequence types (ST15, ST231, and one novel ST [ST-V]), 2 K-locus types (KL112 and KL51), and 2 O-locus types (O2V1 and O2V2). The predominant plasmid replicon types associated with the OXA-232 and rmtF genes were ColKP3 (100%) and IncFIB-like (100%). Our study summarized the genetic characteristics of OXA-232-producing K. pneumoniae circulating in China. The results demonstrate the practical applicability of genomic surveillance and its utility in providing methods to prevent transmission. It alerts us to the urgent need for longitudinal surveillance of these transmissible lineages. IMPORTANCE In recent years, the detection rate of carbapenem-resistant K. pneumoniae has increased and represents a major threat to clinical anti-infective therapy. Compared with KPC-type carbapenemases and NDM-type metallo-β-lactamases, OXA-48 family carbapenemases are another important resistance mechanism mediating bacterial resistance to carbapenems. In this study, we investigated the molecular characteristics of OXA-232 carbapenemase-producing K. pneumoniae isolated from several hospitals to clarify the epidemiological dissemination characteristics of such drug-resistant strains in China.

ABSTRACT: Objectives: Here we describe an IncQ1-like plasmid carrying blaKPC-2 in a new non-Tn4401 element found in Citrobacter werkmanii recovered from coastal water. Methods: In vitro and in silico approaches were used to assess antimicrobial resistance determinants, as well as blaKPC-2 vicinities. Results: The LB-887 isolate showed a multidrug-resistant phenotype and was identified as C. werkmanii. Resistome analysis identified further acquired resistance determinants to β-lactams, aminoglycosides, sulphonamides/trimethoprim, tetracyclines, chloramphenicol, macrolides, rifampicin and fluoroquinolones. Plasmidome included incompatibility groups IncA, IncC2, IncR, Col and IncQ families. The blaKPC-2 was inserted on a new variant of NTEKPC-II, called here NTEKPC-IIe, carried by an InQ1-like plasmid of 7930 kb (pKPC-LB887). NTEKPC-IIe differed from NTEKPC-IId by the complete absence of ISKpn6-tnpA. The InQ1-like backbone harbouring this element had been described in Enterobacterales recovered from clinical and environmental settings. Conclusion: Unravelling genetic structures related to blaKPC dissemination in different settings may provide clues on the main forces driving evolution of this important resistance determinant. Indeed, the occurrence of blaKPC in a new NTEKPC variant from an environmental source highlights the ongoing evolution of this mobile genetic element. In addition, blaKPC carriage on a small and highly mobilizable IncQ plasmid in C. freundii complex from recreational water, similar to others found in clinical isolates, may suggest its relevance for blaKPC-2 dissemination among different compartments.

ABSTRACT The linezolid resistance mediated by optrA has exhibited an increasing trend among Gram-positive bacteria, which greatly limits the treatment options for severe bacterial infections. However, the prevalence of optrA was usually underestimated based on the existing screening methods. In this study, we used a traditional method and an improved method that included a high-salinity condition treatment after enrichment to screen for optrA-carrying bacteria from stool samples from 1,018 healthy donors in Hangzhou, China. The fecal carriage rate of optrA-carrying bacteria was 19.25% when screened by the improved method (196/1,018), which was much higher than that of the traditional method at 5.89% (60/1,018). Enterococci were the majority of the optrA-positive isolates, while five nonenterococcal isolates were also obtained, including two Streptococcus gallolyticus, one Vagococcus lutrae, one Lactococcus garvieae, and one Lactococcus formosensis isolate. Whole-genome sequencing analysis identified four novel OptrA variants, IDKKGPM, IDKKGP, KLDK, and EYDDI, in these isolates, whose optrA-flanking regions with a fexA gene downstream were bounded by different insertion sequences. In conclusion, our optimized method displayed high sensitivity in the detection of optrA-positive bacteria in fecal samples and revealed a high carriage rate in a healthy population. Although enterococci are dominant, multiple optrA-carrying Gram-positive bacteria were also found. IMPORTANCE This study represented an optimized screening approach for the optrA gene, which is an important mechanism of antimicrobial resistance to linezolid as a last resort for the treatment of infections caused by multiresistant Gram-positive bacteria. We revealed a high fecal carriage rate of the optrA gene among adults by this method and reported the first identification of optrA in Lactococcus formosensis as well as the identification of this gene in Vagococcus lutrae and of the poxtA gene in Ligilactobacillus salivarius of human origin, suggesting the wide spread of the optrA gene in the Gram-positive bacterial community.

The appearance of transferable oxazolidinone resistance genes poses a major challenge to public health and environmental safety. These genes not only lead pathogenic bacteria to become resistant to linezolid but also reduce sensitivity to florfenicol, which is widely used in the veterinary field. To verify the dissemination of oxazolidinone resistance genes in enterococcal isolates from pigs at different production stages in a swine farm in China, we collected 355 enterococcal isolates that were resistant to florfenicol from 600 (150 per stage) fresh fecal swabs collected from a swine farm. Through initial PCR screening and whole-genome sequencing, 175 isolates harboring different oxazolidinone resistance genes were identified. All isolates carried the optrA gene. A total of 161 (92%, 161/175) isolates carried only the optrA gene. Three (1.71%, 3/175) isolates carried both the optrA and poxtA genes, and 11 (3.1%, 11/175) isolates contained the optrA gene and poxtA2 and cfr(D) variants. A total of 175 isolates that harbored oxazolidinone resistance genes included 161 E. faecalis, 6 E. faecium, and 8 E. hirae. By sequencing the whole genomes, we found that the 161 isolates of E. faecalis belonged to 28 different STs, including 8 new STs, and the 6 isolates of E. faecium belonged to four different STs, including one new ST. The phylogenetic tree based on SNPs of the core genome showed that both clonal spread and horizontal transfer mediated the diffusion of oxazolidone resistance genes in enterococcal isolates at specific stages in pig farms. Moreover, enterococcal isolates carrying oxazolidone resistance genes could spread from breeding pigs to fattening pigs, while transferable oxazolidone resistance genes in enterococcal isolates could persist on a pig farm throughout all production stages. Representative enterococcal isolates with different oxazolidinone resistance genes were further studied through Nanopore sequencing. We identified a novel plasmid, pM4-80L4 (15,008bp), carrying the poxtA2 and cfr(D) genes in enterococcal isolates at different stages. We also found three different plasmids harboring the poxtA gene with high genetic variation, and all poxtA genes were flanked by two copies of IS1216E elements. In addition, four genetically distinct plasmids carrying the optrA gene were identified, and Tn554 was found to mediate chromosome-localized optrA gene transfer. Our study highlighted that transferable oxazolidinone resistance genes in enterococcal isolates could persist throughout all production stages on a pig farm, and the prevalence and dissemination of oxazolidinone resistance genes in enterococcal isolates from animal farms should be continually monitored. [ABSTRACT FROM AUTHOR]

Dissemination of the Klebsiella pneumoniae carbapenemase (KPC)-encoding gene among Enterobacterales is common but relatively rare in Aeromonas spp. In this study, we characterized two KPC-2-producing Aeromonas hydrophila strains (Ah2101 and Ah2111), each isolated from a patient in different intensive care units (ICUs) of a Chinese hospital. Whole-genome sequencing (WGS) revealed simultaneous carriage of the blaKPC-2 and imiH genes, both of which encode high-level carbapenem resistance in these two A. hydrophila isolates. The two isolates were shown to be clonally related and each isolate harbored two distinguishable blaKPC-2-bearing plasmids, only one of which was transferrable to A. hydrophila, but not Escherichia coli EC600 via conjugation. The genetic element that contains blaKPC-2 in these two plasmids, namely ISKpn27-1blaTEM-1-blaKPC-2-ISKpn6, was structurally identical, commonly detected in Enterobacterales, and associated with Tn3-based transposons. In addition, more than sixty putative genes that encode various virulence factors were identified in these two A. hydrophila isolates. This is the first study that reports clonal dissemination of carbapenem-resistant A. hydrophila strains carrying structurally different blaKPC-2-bearing plasmids. Further investigation is warranted to monitor the future transmission of blaKPC-2-bearing plasmids in A. hydrophila in clinical settings. [ABSTRACT FROM AUTHOR]

The most widely distributed blaCTX-M gene on a global scale is blaCTX-M-15. The dissemination has been associated with clonal spread and different types of mobile genetic elements. The objective of this review was to describe the genetic environments of the blaCTX-M-15 gene detected from Enterobacteriaceae in published literature from Africa. A literature search for relevant articles was performed through PubMed, AJOL, and Google Scholar electronic databases; 43 articles from 17 African countries were included in the review based on the eligibility criteria. Insertion sequences were reported as part of the genetic environment of blaCTX-M-15 gene in 32 studies, integrons in 13 studies, and plasmids in 23 studies. In this review, five insertion sequences including ISEcp1, IS26, orf447, IS903, and IS3 have been detected which are associated with the genetic environment of blaCTX-M-15 in Africa. Seven different genetic patterns were seen in the blaCTX-M-15 genetic environment. Insertion sequence ISEcp1 was commonly located upstream of the end of the blaCTX-M-15 gene, while the insertion sequence orf477 was located downstream. In some studies, ISEcp1 was truncated upstream of blaCTX-M-15 by insertion sequences IS26 and IS3. The class 1 integron (Intl1) was most commonly reported to be associated with blaCTX-M-15 (13 studies), with Intl1/dfrA17–aadA5 being the most common gene cassette array. IncFIA-FIB-FII multi-replicons and IncHI2 replicon types were the most common plasmid replicon types that horizontally transferred the blaCTX-M-15 gene. Aminoglycoside-modifying enzymes, and plasmid-mediated quinolone resistance genes were commonly collocated with the blaCTX-M-15 gene on plasmids. This review revealed the predominant role of ISEcp1, Intl1 and IncF plasmids in the mobilization and continental dissemination of the blaCTX-M-15 gene in Africa.

ABSTRACT: The plasmid-borne fosfomycin resistance gene fosA3 has been identified in Escherichia coli (E. coli) from various animals but has rarely been reported in ducks. In this study, we investigated the fosA3 prevalence and molecular characteristics of fosA3-harboring E. coli strains from ducks in Shandong province of China. In 416 E. coli isolates, 91 (21.88%) were identified as fosA3-bearing strains, and the fosfomycin-resistant phenotype of 88 of the 91 fosA3-harboring strains was successfully transferred to the recipient strains. Seven different genetic structures surrounding the fosA3 gene were detected and 2 new contexts were discovered among the fosA3-carrying E. coli. Twenty fosA3-harboring isolates and their trans-conjugants were randomly selected for pulsed-field gel electrophoresis (PFGE) typing and S1-nuclease PFGE, respectively. The PFGE patterns revealed that the 20 randomly selected fosA3-bearing isolates were not a result of clonal dissemination. S1-PFGE showed that 15 of the 20 randomly selected trans-conjugants carried a single plasmid, and these 15 plasmids that harbored fosA3 (55–190 kb) were distributed into the following replicon types: IncF (n = 11), IncI1 (n = 1), IncN (n = 1), untypable (n = 1), and W-FIC (n = 1). Additionally, as vectors for fosA3 in E. coli, F-:A1:B6, N/ST1, IncI1/ST2, W-FIC, and one untypable plasmid had never been reported before. These observations highlighted the importance of ducks as a reservoir for multidrug-resistant fosA3-carrying E. coli.

Bacterial resistance to β-lactams is mainly attributed to CTX-M-type extended-spectrum β-lactamases (ESBLs). However, the predominant sequence type (ST) of bla CTX-M -carrying Escherichia coli (bla CTX-M -Ec) in chickens, an important food animal, in China and its contribution to human β-lactam resistance are not investigated. In this study, approximately 1808 chicken-derived strains collected from 10 provinces from 2012 to 2020 were screened for bla CTX-M -Ec, and 222 bla CTX-M -Ec were identified. Antimicrobial susceptibility tests, whole genome sequencing and conjugation experiment were performed. All quality-controlled 136 chicken-derived bla CTX-M -Ec and 1193 human-derived bla CTX-M -Ec genomes were downloaded from NCBI and EnteroBase to comprehensively analyze the prevalence of bla CTX-M -Ec in China. bla CTX-M-55 (153/358, 42.7% in chicken isolates; 312/1193, 26.2% in human isolates) and bla CTX-M-14 (92/358, 25.7% in chicken isolates; 450/1193, 37.7% in human isolates) were dominant in bla CTX-M -Ec. The STs of bla CTX-M -Ec were diverse and scattered, with ST155 (n = 21) and ST152 (n = 120) being the most abundant in chicken- and human-derived isolates, respectively. Few examples indicated that chicken- and human-derived bla CTX-M -Ec have 10 or less core genome single nucleotide polymorphisms (cgSNPs). Genetic environment analysis indicated that IS Ecp1 , IS 26 and IS 903B were closely associated with bla CTX-M transfer. The almost identical pc61–55 and pM-64–1161 indicated the possibility of plasmid-mediated transmission of bla CTX-M between humans and chickens. Although the genomes of most bla CTX-M -Ec isolated from chickens and humans were quite different, the prevalence and genetic environment of bla CTX-M variants in both hosts were convergent. CTX-M-mediated resistance is more likely to spread through horizontal gene transmission than bacterial clones. [ABSTRACT FROM AUTHOR]

Min Hao,1,2 Zhen Shen,1,2 Meiping Ye,1,2 Fupin Hu,1,2 Xiaogang Xu,1,2 Yang Yang,1,2 Shi Wu,1,2 Dongfang Lin,1,2 Xiaohua Qin,1,2 Minggui Wang1,2 1Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China; 2Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People’s Republic of ChinaCorrespondence: Xiaohua QinInstitute of Antibiotics, Huashan Hospital, Fudan University, No. 12 Middle Urumuqi Road, Huashan Hospital, Shanghai, People’s Republic of ChinaTel +862152888195Email 0456240@fudan.edu.cnPurpose: This study aimed to evaluate the molecular characteristics and prevalence of clinical carbapenem-resistant Klebsiella aerogenes (CRKA), collected during an outbreak in a Chinese tertiary hospital.Methods: Antimicrobial susceptibility test, using 17 antibiotics, was performed on 14 CRKA isolates. The strains were examined for the presence of β-lactamase genes by PCR, and efflux pump phenotype was determined by efflux pump inhibition test. Presence of outer-membrane porins was examined. Clonal relatedness among the isolates was investigated by pulsed-field gel electrophoresis (PFGE). S1 nuclease-PFGE and plasmid incompatibility group analysis were performed to determine plasmids, and the genetic environment of blaKPC-2 was analyzed. Epidemiological data were collected via chart review.Results: The 14 CRKA isolates were all resistant to carbapenems; five distinct groups (PFGE types A–E) were observed. All 14 isolates carried the blaKPC-2 gene. S1 nuclease-PFGE indicated the size of blaKPC-2-carrying plasmids to range from 20 kb to 200 kb, and the 14 plasmids belonged to various incompatibility groups. The most frequent genetic environment of blaKPC-2 was Tn1721- blaKPC-2-ΔTn3-IS26. PFGE type A group, including 11 KPC-2-producing clinical isolates, was primarily responsible for dissemination.Conclusion: Our findings suggest both transposons and vertical transmission to contribute to the transformation of blaKPC-2. The results strongly suggest strict implementation of infection control of CRKA, in healthcare facilities.Keywords: carbapenem resistance, Klebsiella aerogenes, Klebsiella pneumoniae carbapenemase, plasmid, genetic environment, outbreak

Abstract Background Linezolid-resistant enterococci pose great challenges in clinical practice. The aim of this study is to study the mechanisms underlying the resistance and genetic environment of antimicrobial resistance gene of linezolid-resistant enterococci. Results The linezolid MICs of 16 enterococci were 4 mg/L to 16 mg/L. Four strains belonged to multi-drug resistant (MDR) bacteria. The sequence types (STs) of 13 enterococci strains performed WGS were diverse: 3 ST476, 1 ST86, ST116, ST480, ST59, ST416, ST21, ST67, ST16, ST585 and ST18. None of them carried multi-drug resistance gene cfr. Only one strain had the G2658 T mutation of target 23S rRNA gene. Thirteen (13/16, 81.3%) strains harbored the novel oxazolidinone resistance gene optrA. WGS analysis showed that the optrA gene was flanked by sequence IS1216E insertion in 13 strains, and optrA was adjacent to transposons Tn558 in two strains and Tn554 in one strain. The optrA gene was identified to be co-localized with fexA, the resistance genes mediated florfenicol resistance in 13 strains, and ermA1, the resistance genes mediated erythromycin resistance in 9 strains, indicating that linezolid-resistant strains may be selected due to non-oxazolidinone antibiotics (i.e. macrolides and florfenicol) usage. Conclusion Our findings demonstrate the high diversity of optrA-carrying genetic platforms. The mobile genetic elements (MGEs) may play an important role in the dissemination of optrA into the enterococci isolates of human origin. The genetic evidence of transferable feature and co-selection of optrA should be gave more attention in clinical practice.

Yan-Yan Hu, Qi Wang, Qiao-Ling Sun, Gong-Xiang Chen, Rong Zhang2nd Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang University, Hangzhou, People’s Republic of ChinaAbstract: A carbapenem-resistant Pseudomonas aeruginosa strain PA1011 (ST463) was isolated from a patient in a surgical intensive care unit. PCR detection showed that PA1011 carried the blaKPC-2 gene. A plasmid was isolated and sequenced using the Illumina NextSeq 500 and PacBio RSII sequencing platforms. The plasmid was named pPA1011 and carried the carbapenem-resistant gene blaKPC-2. pPA1011 was a 62,793 bp in length with an average G+C content of 58.8%. It was identified as a novel plasmid and encoded a novel genetic environment of blaKPC-2 gene (ΔIS6-Tn3-ISKpn8-blaKPC-2-ISKpn6-IS26).Keywords: plasmid, genetic environment, KPC, ST463, Pseudomonas aeruginosa

The most widely distributed blaCTX-M gene on a global scale is blaCTX-M-15. The dissemination has been associated with clonal spread and different types of mobile genetic elements. The objective of this review was to describe the genetic environments of the blaCTX-M-15 gene detected from Enterobacteriaceae in published literature from Africa. A literature search for relevant articles was performed through PubMed, AJOL, and Google Scholar electronic databases; 43 articles from 17 African countries were included in the review based on the eligibility criteria. Insertion sequences were reported as part of the genetic environment of blaCTX-M-15 gene in 32 studies, integrons in 13 studies, and plasmids in 23 studies. In this review, five insertion sequences including ISEcp1, IS26, orf447, IS903, and IS3 have been detected which are associated with the genetic environment of blaCTX-M-15 in Africa. Seven different genetic patterns were seen in the blaCTX-M-15 genetic environment. Insertion sequence ISEcp1 was commonly located upstream of the end of the blaCTX-M-15 gene, while the insertion sequence orf477 was located downstream. In some studies, ISEcp1 was truncated upstream of blaCTX-M-15 by insertion sequences IS26 and IS3. The class 1 integron (Intl1) was most commonly reported to be associated with blaCTX-M-15 (13 studies), with Intl1/dfrA17-aadA5 being the most common gene cassette array. IncFIA-FIB-FII multi-replicons and IncHI2 replicon types were the most common plasmid replicon types that horizontally transferred the blaCTX-M-15 gene. Aminoglycoside-modifying enzymes, and plasmid-mediated quinolone resistance genes were commonly collocated with the blaCTX-M-15 gene on plasmids. This review revealed the predominant role of ISEcp1, Intl1 and IncF plasmids in the mobilization and continental dissemination of the blaCTX-M-15 gene in Africa. [ABSTRACT FROM AUTHOR]

To analyze the characteristics of fosA and fosA3 in Enterobacter cloacae isolated from aspirated and catheterized urine culture specimens of companion pets in Taiwan. A total of 19 E. cloacae isolates from pets with urinary tract infection were screened for the presence of fosA, fosA3, and fosC2 and for the genetic context of them by PCR amplification and sequencing. The transferability, resistance phenotypes, plasmid replicon typing properties and genetic environments of fosA- and/or fosA3-positive strains were characterized. Five E. cloacae isolates were positive for fosA and three coharbored fosA and fosA3. No fosC determinant was detected. Transconjugants of fosA3 were successfully acquired, while the acquisition of fosA transconjugants was failed. The minimum inhibitory concentrations (MICs) of the three fosA3-positive isolates and their transconjugants were ≥256 mg/L, whereas the MICs of the five fosA-positive isolates ranged from 64 mg/L to 256 mg/L. Three plasmid replicons (InCFrepB, InCL/M, and InCHI2) were identified in fosA- and fosA3-positive E. cloacae isolates. Different genetic contexts lay in the downstream region of fosA and fosA3, respectively. Eight distinct patterns based on the similarity value of more than 80% were typed for all the 8 fosA-positive isolates. In conclusion, the fosA concomitant with fosA3 were found in E. cloacae isolates. The fosA3 not only exhibits stronger activity of inactivating fosfomycin than fosA but also possesses stronger potential to spread than fosA. Different genetic backgrounds exist in these fosA- and fosA3-positive isolates, and different mobile elements may confer the dissemination of fosA and fosA3. [ABSTRACT FROM AUTHOR]

Carbapenem resistance in Enterobacteriaceae members has become a major challenge, and the genetic environment of bla KPC, encoding Klebsiella pneumoniae carbapenemases, has not been fully clarified in China. In this study, we aimed to explore the genetic environment of bla KPC in 25 carbapenem-resistant E. coli isolates from hospitals in Hangzhou Province, China. Antimicrobial susceptibility against 22 common antimicrobial agents was tested. Polymerase chain reaction (PCR) analysis was performed for screening of the resistent genes, such as bla KPC, bla CTX-M, bla TEM, bla SHV, bla NDM, qnrA , qnrB , qnrS, aac(6')-Ib, armA and rmtB. The genetic environment of bla KPC were determinedin one isolate. bla KPC was detected by PCR in all the clinical E. coli isolates. There were no strains carrying bla NDM, qnrA and armA. The genetic environment of bla KPC showed that bla KPC dissemination is plasmid mediated and that it is located in the Tn 3 –Tn 4401 transposon complex. Encoding of bla KPC-2 was responsible for carbapenem resistance in the 25 E. coli isolates. The genetic environment of bla KPC was characterized by the Tn 3 –Tn 4401 complex. Our findings may provide a theoretical basis for clinical drug-resistance monitoring, anti-infection treatment and hospital infection control. [ABSTRACT FROM AUTHOR]

Objectives: The emergence of the florfenicol resistance gene fexA in Campylobacter poses a serious threat to public health, but the extent of the spread of fexA in Campylobacter from various hosts has not been well understood. This study aimed to investigate the fexA in Campylobacter isolates from different hosts., Methods: PCR was used to identify fexA-positive Campylobacter from different hosts during 2008-2019 in China, and the fexA-positive isolates were characterized by susceptibility tests, whole-genome sequencing, and natural transformation., Results: A total of 69 (2.54%, 69/2721) fexA-positive Campylobacter were identified, and the fexA-positive isolates increased remarkably (0.42%-16.90%) since it was first detected in 2010. By source, the 69 isolates were obtained from chickens (3.57%, 57/1595), geese (3.43%, 7/204), ducks (1.02%, 2/197), and environments (2.86%, 3/105); the fexA-positive isolates were not isolated in humans and pigs. In addition to fexA, these isolates also carried other antimicrobial resistance genes and exhibited multidrug resistance. Whole-genome sequencing analysis showed the fexA gene can disseminate clonally or horizontally via either multidrug resistance genomic islands or insertion sequences among the Campylobacter. The genetic structure IS1216-∆ISEfa11-hp-fexA-NAD(P)H-∆ISEfa11-IS1216 was conserved and widespread in the Campylobacter of various origins, and the IS1216 can form fexA-carrying circular intermediates, emphasizing that IS1216 plays an important role in the spread of fexA in Campylobacter., Conclusions: This study indicates the wide spread of fexA-positive Campylobacter in poultry and environments. Because multidrug resistance genomic islands and IS1216 can facilitate the transmission of fexA, systematic surveillance should be implemented to prevent the spread of fexA to humans., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

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A carbapenem-resistant Pseudomonas aeruginosa strain PA1011 (ST463) was isolated from a patient in a surgical intensive care unit. PCR detection showed that PA1011 carried the blaKPC-2 gene. A plasmid was isolated and sequenced using the Illumina NextSeq 500 and PacBio RSII sequencing platforms. The plasmid was named pPA1011 and carried the carbapenem-resistant gene blaKPC-2. pPA1011 was a 62,793 bp in length with an average G+C content of 58.8%. It was identified as a novel plasmid and encoded a novel genetic environment of blaKPC-2 gene (ΔIS6-Tn3-ISKpn8-blaKPC-2-ISKpn6-IS26). [ABSTRACT FROM AUTHOR]

The predominance of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae was caused by the spread of ST258 clone. In Latin America, KPC was reported in 2006, with the isolation of genetically unrelated K. pneumoniae in Colombia. Since then, the expansion of blaKPC in either K. pneumoniae ST258 or other Enterobacteriaceae (ETB) species was increasingly reported. In this study, we characterized 89 KPC-producing Escherichia coli, Klebsiella oxytoca, Serratia marcescens, and Citrobacter freundii that were received between 2010 and 2014. The results revealed that all isolates harbored blaKPC-2. Moreover, the dissemination of KPC by non-K. pneumoniae was mainly caused by the dispersion of ETB mostly genetically unrelated. E. coli is a community pathogen that may serve as the vehicle for the spread of KPC into community settings. Recently, KPC was detected in E. coli ST131, an international epidemic and multidrug-resistant clone. We found that 5/29 KPC-producing E. coli belonged to ST131 and four were blaCTXM-15 producers. The detection of blaKPC in ST131 should be closely monitored to prevent further dissemination. The blaKPC is generally located within Tn4401 transposon capable of mobilization through transposition found in plasmids in ST258. Less is known about the diversity of blaKPC genetic elements that disseminate horizontally among other species of ETB. We found that 16/29 E. coli and 2/18 S. marcescens harbored blaKPC-2 in Tn4401a. In 71 isolates, blaKPC-2 was located amidst diverse Tn3-derived genetic elements bearing non-Tn4401 structure. Further studies on the plasmids that encode blaKPC-2 in these clinical isolates may provide additional insight into its transmission mechanisms. [ABSTRACT FROM AUTHOR]

The presence of antibiotic resistance genes (ARGs) including those expressing ESBLs and AmpC-β-lactamases in Escherichia coli inhabiting the aquatic environments is a serious health problem. The situation is further complicated by the fact that ARGs can be easily transferred among bacterial species with the help of mobile genetic elements – plasmids, integrons, insertion sequences (IS), and transposons. Therefore, the analysis of genetic environment and mobile genetic elements associated with ARGs is important as these provide useful information about the epidemiology of these genes. In our previous study, we had reported presence of various β-lactam resistance genes present in E. coli strains inhabiting the river Yamuna traversing the National Capital Territory of Delhi (India). In the present study, we have analyzed the genetic environment of three ARGs blaTEM-1, blaCTX-M-15, and blaCMY -42 of those E. coli strains. The structure of class 1 integrons and their gene cassettes was also analyzed. Insertion sequence IS26 was present upstream of blaTEM-1, ISEcp1 was present upstream of blaCTXM-15 gene and orf477 was present downstream of blaCTXM-15. ISEcp1 was also present upstream of blaCMY -42 and, blc and sugE genes were present in the downstream region of this gene. Thus, the overall genetic environment surrounding these genes was similar to that reported from E. coli strains isolated globally. Conjugation assays, isolation and analysis of plasmid DNA of the transconjugants indicated that blaTEM-1, blaCTX-M-15, blaCMY -42 and class 1 integron were plasmid-mediated and possibly transmit between genera through horizontal gene transfer (HGT). This might lead to dissemination of antimicrobial resistance genes in aquatic environment. The work embodied in this paper is the first describing the genetic environment of bla and integrons in aquatic E. coli isolated from India. [ABSTRACT FROM AUTHOR]

The increasing incidence of carbapenem-resistant Enterobacteriaceae has become a challenge for clinical therapy. In our study, we analysed the molecular characteristics of imipenem-hydrolyzing β-lactamase (IMI) in Enterobacteriaceae isolates. Two reported clinical isolates, the IMI-3-producing Raoultella ornithinolytica RJ46C and the IMI-2-producing Escherichia coli RJ18 were identified in our retrospective review of isolates collected from June 2010 to June 2013, both isolates were resistant to carbapenem but sensitive to expanded-spectrum cephalosporins. The bla IMI gene was located on different ∼170-kb plasmids in both isolates. The bla IMI-3 gene was carried by the plasmid pRJ46C, which was extracted from the transconjugant and identified to be a 166,620-bp conjugative IncFII Y plasmid that contained 193 open reading frames, including replication-, plasmid conjugal transfer-, partitioning-, and mobilization-associated structures. The bla IMI-3 gene was located on a 15-kb region with a completely inverted sequence relative to that of plasmid pGA45, two IS Ecl1 -like elements containing two 33-bp complete inverted repeats were in an inverted orientation on both sides of the 15-kb region. We identified this typical structure as a novel composite transposon named Tn 6306 , indicating the occurrence of transposition. In addition, the bla IMI-2 -carrying pRJ18 was an IncFIB plasmid, and a similar IS Ecl1 -like element was identified in an inverted direction upstream of IMI-2 in pRJ18. The identification of bla IMI in R. ornithinolytica and E. coli highlights the diversity of spreading carbapenemases in Enterobacteriaceae between hospitals and the environment in China. The novel transposon Tn 6306 , and other insert sequences, may play important roles in bla IMI mobilization. [ABSTRACT FROM AUTHOR]

With the abuse of macrolide, lincosamide, and streptogramin (MLS), the traditionally safe bifidobacterial strains in the human intestine could serve as a reservoir of MLS resistance genes. In this study, the erm (X) gene was detected in 29 MLS-resistant strains and one MLS-susceptible strain among 92 bifidobacterial strains of human origin. This study is the first to report erm (X)-mediated MLS resistance in Bifidobacterium pseudocatenulatum , Bifidobacterium breve and Bifidobacterium bifidum . The insertion sequences (ISs) flanking antibiotic resistance (AR) genes (i.e., the genetic environment of AR genes) could contribute to the horizontal spreading of AR. However, the potential transferability of erm (X) in bifidobacteria has not been previously verified. Here, we retrieved four genetic environments (I–IV) of erm (X) from 30 erm (X)-positive bifidobacterial strains. This study is the first to identify the erm (X) gene in three new genetic environments (II, III and IV) in bifidobacteria. The erm (X) gene was individually flanked by IS 1249 or IS 3 in genetic environments I, II and IV and was simultaneously flanked by IS 1249 and IS 3 elements in genetic environment III. Only the transfer of erm (X) from genetic environment III simultaneously flanked by IS 1249 and IS 3 elements was successfully observed in filter mating experiments. These findings indicate a synergic effect of IS 1249 and IS 3 elements in the transfer of erm (X) in bifidobacteria, and further reveal that the various genetic environments of erm (X) result in significant differences in the transferability of erm (X) in bifidobacteria. [ABSTRACT FROM AUTHOR]

Two Klebsiella pneumoniae isolates (Kpc1 and Kpc2) were obtained from liver samples of seven dead chickens and identified with Vitek-32 automated identification system. Antimicrobial susceptibilities were determined by the microdilution broth method. Detection of genes encoding class A β-lactamases was performed by PCR amplification, and cloning of the ESBL gene was by plasmid restriction and fragments ligation. Conjugation assay, transformation experiments and plasmid profile analysis were performed. The incompatibility group of ESBL-carrying plasmid was determined by the PCR-based replicon typing method. Lastly, the genetic environment was analysed by direct sequencing of the DNA surrounding the ESBL gene. The genes associated with tetracycline and gentamicin resistance were also sought by PCR. The results revealed that the ESBL phenotype-negative strain Kpc2 only showed resistance to ampicillin, amoxicillin, tetracycline, and doxycycline and carried blaTEM-1 and tet(A) genes. The ESBL-producing strain Kpc1 exhibited multidrug resistant phenotype and harbored blaTEM-1, blaCTX-M-14, tet(A), tet(B), and rmtB genes. K. pneumoniae Kpc1 contained four plasmids with molecular sizes of approximately 59, 6.9, 2.8, and 1.6 kb, but only a 59-kb plasmid, carried blaTEM-1 and blaCTX-M-14 genes, was observed in its transconjugant. The incompatibility group of plasmid carrying blaCTX-M-14 gene could not be determined. The blaCTX-M-14 gene was flanked upstream by an ISEcp1 insertion sequence and downstream by an IS903 element. This work shows that CTX-M-14 is present in K. pneumoniae isolates from chickens in China. The blaCTX-M-14 gene was associated with an upstream ISEcp1 insertion sequence. Our results underline the need for continuous surveillance of the prevalence and evolution of this CTX-M-type β-lactamase in China.

OXA-232 carbapenemase is becoming a threat in China due to its high prevalence, mortality, and limited treatment options. However, little information is available on the impact of OXA-232-producing Klebsiella pneumoniae in China. This study aims to characterize the clonal relationships, the genetic mechanisms of resistance, and the virulence of OXA-232-producing K. pneumoniae isolates in China. We collected 81 OXA-232-producing K. pneumoniae clinical isolates from 2017 to 2021. Antimicrobial susceptibility testing was performed using the broth microdilution method. Capsular types, multilocus sequence types, virulence genes, antimicrobial resistance (AMR) determinants, plasmid replicon types, and single-nucleotide polymorphism (SNP) phylogeny were inferred from whole-genome sequences. OXA-232-producing K. pneumoniae strains were resistant to most antimicrobial agents. These isolates showed partial differences in susceptibility to carbapenems: all strains were resistant to ertapenem, while the resistance rates to imipenem and meropenem were 67.9% and 97.5%, respectively. Sequencing and capsular diversity analysis of the 81 K. pneumoniae isolates revealed 3 sequence types (ST15, ST231, and one novel ST [ST-V]), 2 K-locus types (KL112 and KL51), and 2 O-locus types (O2V1 and O2V2). The predominant plasmid replicon types associated with the OXA-232 and rmtF genes were ColKP3 (100%) and IncFIB-like (100%). Our study summarized the genetic characteristics of OXA-232-producing K. pneumoniae circulating in China. The results demonstrate the practical applicability of genomic surveillance and its utility in providing methods to prevent transmission. It alerts us to the urgent need for longitudinal surveillance of these transmissible lineages. IMPORTANCE In recent years, the detection rate of carbapenem-resistant K. pneumoniae has increased and represents a major threat to clinical anti-infective therapy. Compared with KPC-type carbapenemases and NDM-type metallo-β-lactamases, OXA-48 family carbapenemases are another important resistance mechanism mediating bacterial resistance to carbapenems. In this study, we investigated the molecular characteristics of OXA-232 carbapenemase-producing K. pneumoniae isolated from several hospitals to clarify the epidemiological dissemination characteristics of such drug-resistant strains in China., Competing Interests: The authors declare no conflict of interest.

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Capnocytophaga spp. are commensal bacteria involved in oral and systemic diseases, with a variable susceptibility to beta-lactams. The cfxA gene expression level was assessed using quantitative RT-PCR, and reasons of the observed misexpression were discussed, as insertion of foreign genetic material, contributing to dissemination and evolution of antibiotic resistance genes. [ABSTRACT FROM AUTHOR]

Background: Chromosomally encoded AmpC β-lactamases may be acquired by transmissible plasmids which consequently can disseminate into bacteria lacking or poorly expressing a chromosomal blaAmpC gene. Nowadays, these plasmid-mediated AmpC β-lactamases are found in different bacterial species, namely Enterobacteriaceae, which typically do not express these types of β-lactamase such as Klebsiella spp. or Escherichia coli. This study was performed to characterize two E. coli isolates collected in two different Portuguese hospitals, both carrying a novel CMY-2-type β-lactamase-encoding gene. Findings: Both isolates, INSRA1169 and INSRA3413, and their respective transformants, were non-susceptible to amoxicillin, amoxicillin plus clavulanic acid, cephalothin, cefoxitin, ceftazidime and cefotaxime, but susceptible to cefepime and imipenem, and presented evidence of synergy between cloxacilin and cefoxitin and/or ceftazidime. The genetic characterization of both isolates revealed the presence of blaCMY-46 and blaCMY-50 genes, respectively, and the following three resistance-encoding regions: a Citrobacter freundii chromosome-type structure encompassing a blc-sugE-blaCMY-2-type-ampR platform; a sul1-type class 1 integron with two antibiotic resistance gene cassettes (dfrA1 and aadA1); and a truncated mercury resistance operon. Conclusions: This study describes two new blaCMY-2-type genes in E. coli isolates, located within a C. freundii-derived fragment, which may suggest their mobilization through mobile genetic elements. The presence of the three different resistance regions in these isolates, with diverse genetic determinants of resistance and mobile elements, may further contribute to the emergence and spread of these genes, both at a chromosomal or/and plasmid level. [ABSTRACT FROM AUTHOR]

Background: Strains of Escherichia coli that are non-typeable by pulsed-field gel electrophoresis (PFGE) due to in-gel degradation can influence their molecular epidemiological data. The DNA degradation phenotype (Dnd+) is mediated by the dnd operon that encode enzymes catalyzing the phosphorothioation of DNA, rendering the modified DNA susceptible to oxidative cleavage during a PFGE run. In this study, a PCR assay was developed to detect the presence of the dnd operon in Dnd+ E. coli strains and to improve their typeability. Investigations into the genetic environments of the dnd operon in various E. coli strains led to the discovery that the dnd operon is harboured in various diverse genomic islands. Results: The dndBCDE genes (dnd operon) were detected in all Dnd+ E. coli strains by PCR. The addition of thiourea improved the typeability of Dnd+ E. coli strains to 100% using PFGE and the Dnd+ phenotype can be observed in both clonal and genetically diverse E. coli strains. Genomic analysis of 101 dnd operons from genome sequences of Enterobacteriaceae revealed that the dnd operons of the same bacterial species were generally clustered together in the phylogenetic tree. Further analysis of dnd operons of 52 E. coli genomes together with their respective immediate genetic environments revealed a total of 7 types of genetic organizations, all of which were found to be associated with genomic islands designated dnd-encoding GIs. The dnd-encoding GIs displayed mosaic structure and the genomic context of the 7 islands (with 1 representative genome from each type of genetic organization) were also highly variable, suggesting multiple recombination events. This is also the first report where two dnd operons were found within a strain although the biological implication is unknown. Surprisingly, dnd operons were frequently found in pathogenic E. coli although their link with virulence has not been explored. Conclusion: Genomic islands likely play an important role in facilitating the horizontal gene transfer of the dnd operons in E. coli with 7 different types of islands discovered so far. [ABSTRACT FROM AUTHOR]

The linezolid resistance mediated by optrA has exhibited an increasing trend among Gram-positive bacteria, which greatly limits the treatment options for severe bacterial infections. However, the prevalence of optrA was usually underestimated based on the existing screening methods. In this study, we used a traditional method and an improved method that included a high-salinity condition treatment after enrichment to screen for optrA -carrying bacteria from stool samples from 1,018 healthy donors in Hangzhou, China. The fecal carriage rate of optrA -carrying bacteria was 19.25% when screened by the improved method (196/1,018), which was much higher than that of the traditional method at 5.89% (60/1,018). Enterococci were the majority of the optrA -positive isolates, while five nonenterococcal isolates were also obtained, including two Streptococcus gallolyticus, one Vagococcus lutrae, one Lactococcus garvieae, and one Lactococcus formosensis isolate. Whole-genome sequencing analysis identified four novel OptrA variants, IDKKGPM, IDKKGP, KLDK, and EYDDI, in these isolates, whose optrA- flanking regions with a fexA gene downstream were bounded by different insertion sequences. In conclusion, our optimized method displayed high sensitivity in the detection of optrA -positive bacteria in fecal samples and revealed a high carriage rate in a healthy population. Although enterococci are dominant, multiple optrA -carrying Gram-positive bacteria were also found. IMPORTANCE This study represented an optimized screening approach for the optrA gene, which is an important mechanism of antimicrobial resistance to linezolid as a last resort for the treatment of infections caused by multiresistant Gram-positive bacteria. We revealed a high fecal carriage rate of the optrA gene among adults by this method and reported the first identification of optrA in Lactococcus formosensis as well as the identification of this gene in Vagococcus lutrae and of the poxtA gene in Ligilactobacillus salivarius of human origin, suggesting the wide spread of the optrA gene in the Gram-positive bacterial community.

The appearance of transferable oxazolidinone resistance genes poses a major challenge to public health and environmental safety. These genes not only lead pathogenic bacteria to become resistant to linezolid but also reduce sensitivity to florfenicol, which is widely used in the veterinary field. To verify the dissemination of oxazolidinone resistance genes in enterococcal isolates from pigs at different production stages in a swine farm in China, we collected 355 enterococcal isolates that were resistant to florfenicol from 600 (150 per stage) fresh fecal swabs collected from a swine farm. Through initial PCR screening and whole-genome sequencing, 175 isolates harboring different oxazolidinone resistance genes were identified. All isolates carried the optrA gene. A total of 161 (92%, 161/175) isolates carried only the optrA gene. Three (1.71%, 3/175) isolates carried both the optrA and poxtA genes, and 11 (3.1%, 11/175) isolates contained the optrA gene and poxtA2 and cfr(D) variants. A total of 175 isolates that harbored oxazolidinone resistance genes included 161 E. faecalis , 6 E. faecium , and 8 E. hirae . By sequencing the whole genomes, we found that the 161 isolates of E. faecalis belonged to 28 different STs, including 8 new STs, and the 6 isolates of E. faecium belonged to four different STs, including one new ST. The phylogenetic tree based on SNPs of the core genome showed that both clonal spread and horizontal transfer mediated the diffusion of oxazolidone resistance genes in enterococcal isolates at specific stages in pig farms. Moreover, enterococcal isolates carrying oxazolidone resistance genes could spread from breeding pigs to fattening pigs, while transferable oxazolidone resistance genes in enterococcal isolates could persist on a pig farm throughout all production stages. Representative enterococcal isolates with different oxazolidinone resistance genes were further studied through Nanopore sequencing. We identified a novel plasmid, pM4-80 L4 (15,008 bp), carrying the poxtA2 and cfr(D) genes in enterococcal isolates at different stages. We also found three different plasmids harboring the poxtA gene with high genetic variation, and all poxtA genes were flanked by two copies of IS 1216E elements. In addition, four genetically distinct plasmids carrying the optrA gene were identified, and Tn 554 was found to mediate chromosome-localized optrA gene transfer. Our study highlighted that transferable oxazolidinone resistance genes in enterococcal isolates could persist throughout all production stages on a pig farm, and the prevalence and dissemination of oxazolidinone resistance genes in enterococcal isolates from animal farms should be continually monitored., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Huang, Bai, Wang, Yang, Zhang, Chen and Wang.)

The plasmid-borne fosfomycin resistance gene fosA3 has been identified in Escherichia coli ( E. coli) from various animals but has rarely been reported in ducks. In this study, we investigated the fosA3 prevalence and molecular characteristics of fosA3 -harboring E. coli strains from ducks in Shandong province of China. In 416 E. coli isolates, 91 (21.88%) were identified as fosA3 -bearing strains, and the fosfomycin-resistant phenotype of 88 of the 91 fosA3 -harboring strains was successfully transferred to the recipient strains. Seven different genetic structures surrounding the fosA3 gene were detected and 2 new contexts were discovered among the fosA3 -carrying E. coli. Twenty fosA3 -harboring isolates and their trans-conjugants were randomly selected for pulsed-field gel electrophoresis (PFGE) typing and S1-nuclease PFGE, respectively. The PFGE patterns revealed that the 20 randomly selected fosA3 -bearing isolates were not a result of clonal dissemination. S1-PFGE showed that 15 of the 20 randomly selected trans-conjugants carried a single plasmid, and these 15 plasmids that harbored fosA3 (55–190 kb) were distributed into the following replicon types: IncF (n = 11), IncI1 (n = 1), IncN (n = 1), untypable (n = 1), and W-FIC (n = 1). Additionally, as vectors for fosA3 in E. coli , F-:A1:B6, N/ST1, IncI1/ST2, W-FIC, and one untypable plasmid had never been reported before. These observations highlighted the importance of ducks as a reservoir for multidrug-resistant fosA3 -carrying E. coli. [ABSTRACT FROM AUTHOR]

• 8.6% (19/221) of pan-aminoglycoside-resistant Pseudomonas aeruginosa had 16S RMTase genes. • 16S RMTase gene variants rmtB4, rmtD3 and rmtF2 were detected. • 89.5% (17/19) of 16S RMTase gene-positive isolates harboured a carbapenemase gene. • P. aeruginosa 'high-risk' clones ST357, ST654 and ST773 harboured 16S RMTase genes. • Novel genetic environments for rmtB1, rmtC and rmtF2 were identified. 16S rRNA methyltransferase (16S RMTase) genes confer high-level aminoglycoside resistance, reducing treatment options for multidrug-resistant Gram-negative bacteria. Pseudomonas aeruginosa isolates (n = 221) exhibiting high-level pan-aminoglycoside resistance (amikacin, gentamicin and tobramycin MICs ≥64, ≥32 and ≥32 mg/L, respectively) were screened for 16S RMTase genes to determine their occurrence among isolates submitted to a national reference laboratory from December 2003 to December 2015. 16S RMTase genes were identified using two multiplex PCRs, and whole-genome sequencing (WGS) was used to identify other antibiotic resistance genes, sequence types (STs) and the genetic environment of 16S RMTase genes. 16S RMTase genes were found in 8.6% (19/221) of isolates, with rmtB4 (47.4%; 9/19) being most common, followed by rmtD3 (21.1%; 4/19), rmtF2 (15.8%; 3/19) and single isolates harbouring rmtB1, rmtC and rmtD1. Carbapenemase genes were found in 89.5% (17/19) of 16S RMTase-positive isolates, with bla VIM (52.9%; 9/17) being most common. 16S RMTase genes were found in 'high-risk' clones known to harbour carbapenemase genes (ST233, ST277, ST357, ST654 and ST773). Analysis of the genetic environment of 16S RMTase genes identified that IS 6100 was genetically linked to rmtB1 ; IS 91 to rmtB4, rmtC or rmtD3; IS CR14 to rmtD1 ; and rmtF2 was linked to Tn 3 , IS 91 or Tn 1721. Although 16S RMTase genes explained only 8.6% of pan-aminoglycoside resistance in the P. aeruginosa isolates studied, the association of 16S RMTase genes with carbapenemase-producers and 'high-risk' clones highlights that continued surveillance is required to monitor spread as well as the importance of suppressing the emergence of dually-resistant clones in hospital settings. [ABSTRACT FROM AUTHOR]

Abstract: Characterisation of extended-spectrum β-lactamase (ESBL) genes and their genetic environments as well as the presence of integrons were analysed in nine Klebsiella pneumoniae and two Escherichia coli ESBL-positive isolates recovered in the Centre of Bone Marrow Transplantation of Tunisia. All strains harboured the bla CTX-M-15 gene and presented minimum inhibitory concentrations for cefotaxime and ceftazidime of 256–1024mgL−1 and 16–512mgL−1, respectively, and eight of them showed different pulsed-field gel electrophoresis patterns. The bla OXA-1 and bla TEM-1 genes were detected in eight and ten strains, respectively. In addition, bla SHV-1, bla SHV-11 and bla SHV-27 were found in six, one and one K. pneumoniae strains, respectively. The new variant bla SHV-103 was characterised in one K. pneumoniae strain. The intI1 gene was detected in eight K. pneumoniae strains and the dfrA5 + ereA2 and aadA gene cassettes were found in one and five strains, respectively. All strains harboured a 70kb plasmid, and its transference in addition to bla CTX-M-15, bla TEM-1b and bla OXA-1 genes was demonstrated from three K. pneumoniae to E. coli. ISEcp1 and orf477 were located upstream and downstream, respectively, of the bla CTX-M-15 gene in 10 strains. The occurrence of the bla CTX-M-15 gene in unrelated strains might have originated from the dissemination of mobile genetic elements in which ISEcp1 may have played an important role. [Copyright &y& Elsevier]

The risks of systemic lupus erythematosus (SLE) are known to vary considerably with ethnic origin. Prevalence of lupus is increased in African-American, Afro-Caribbean, Native American, Asian Indian, Polynesian and Chinese populations compared with people of European descent. The consistency with which high prevalence of lupus occurs in these populations descent living in different environments suggests that genetic factors are likely to underlie the high risk in this group. However the increased risk of lupus in high risk groups such as West Africans compared with Europeans does not appear to be accounted for by differences in allele frequencies at any of the loci where associations with SLE have been found, including those in the HLA region. To date the contribution of environmental factors to a complex disease such as lupus is still not fully understood. This article explores possible environmental risk factors for SLE in high risk ethnic groups. Smoking, occupational exposures to silica and exposure to infection in childhood may explain some non-genetic risk factors for SLE in these groups. [ABSTRACT FROM AUTHOR]

Twenty-four non-clonally related enterobacterial isolates producing the emerging CTX-M-type extended-spectrum β-lactamases were recovered from several countries including France, India, Poland, and Turkey. They had been isolated from 2000 to 2003. β-Lactamases CTX-M-2, CTX-M-3, CTX-M-10, CTX-M-14 and CTX-M-15 were identified. Most of the isolates produced β-lactamase CTX-M-15. Insertion sequence ISEcp1 was found upstream of blaCTX-M-3, blaCTX-M-10, blaCTX-M-14 and blaCTX-M-15 genes. A sequence similar to the inverted right repeat of ISEcp1 was identified downstream of blaCTX-M-3, blaCTX-M-10 and blaCTX-M-15genes suggesting the mobilization of these β-lactamase genes by transposition events. In addition, Orf513 was identified upstream of the blaCTX-M-2 gene. This work further underlined widespread of blaCTX-M-15gene associated with ISEcp1. [Copyright &y& Elsevier]

Dissemination of the Klebsiella pneumoniae carbapenemase (KPC)-encoding gene among Enterobacterales is common but relatively rare in Aeromonas spp. In this study, we characterized two KPC-2-producing Aeromonas hydrophila strains (Ah2101 and Ah2111), each isolated from a patient in different intensive care units (ICUs) of a Chinese hospital. Whole-genome sequencing (WGS) revealed simultaneous carriage of the bla KPC-2 and imiH genes, both of which encode high-level carbapenem resistance in these two A. hydrophila isolates. The two isolates were shown to be clonally related and each isolate harbored two distinguishable bla KPC-2 -bearing plasmids, only one of which was transferrable to A. hydrophila , but not Escherichia coli EC600 via conjugation. The genetic element that contains bla KPC-2 in these two plasmids, namely IS Kpn27 -Δ bla TEM-1 - bla KPC-2 -IS Kpn6 , was structurally identical, commonly detected in Enterobacterales, and associated with Tn 3 -based transposons. In addition, more than sixty putative genes that encode various virulence factors were identified in these two A. hydrophila isolates. This is the first study that reports clonal dissemination of carbapenem-resistant A. hydrophila strains carrying structurally different bla KPC-2 -bearing plasmids. Further investigation is warranted to monitor the future transmission of bla KPC-2 -bearing plasmids in A. hydrophila in clinical settings., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Xu, Shen, Zhang and Cai.)

Objectives: Here we describe an IncQ1-like plasmid carrying bla KPC-2 in a new non-Tn4401 element found in Citrobacter werkmanii recovered from coastal water., Methods: In vitro and in silico approaches were used to assess antimicrobial resistance determinants, as well as bla KPC-2 vicinities., Results: The LB-887 isolate showed a multidrug-resistant phenotype and was identified as C. werkmanii. Resistome analysis identified further acquired resistance determinants to β-lactams, aminoglycosides, sulphonamides/trimethoprim, tetracyclines, chloramphenicol, macrolides, rifampicin and fluoroquinolones. Plasmidome included incompatibility groups IncA, IncC2, IncR, Col and IncQ families. The bla KPC-2 was inserted on a new variant of NTE KPC -II, called here NTE KPC -IIe, carried by an InQ1-like plasmid of 7930 kb (pKPC-LB887). NTE KPC -IIe differed from NTE KPC -IId by the complete absence of ISKpn6-tnpA. The InQ1-like backbone harbouring this element had been described in Enterobacterales recovered from clinical and environmental settings., Conclusion: Unravelling genetic structures related to bla KPC dissemination in different settings may provide clues on the main forces driving evolution of this important resistance determinant. Indeed, the occurrence of bla KPC in a new NTE KPC variant from an environmental source highlights the ongoing evolution of this mobile genetic element. In addition, bla KPC carriage on a small and highly mobilizable IncQ plasmid in C. freundii complex from recreational water, similar to others found in clinical isolates, may suggest its relevance for bla KPC-2 dissemination among different compartments., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Introduction. The 16S rRNA methyltransferase (16S RMTase) gene armA is the most common mechanism conferring high-level aminoglycoside resistance in Acinetobacter baumannii , although rmtA , rmtB , rmtC , rmtD and rmtE have also been reported. Hypothesis/Gap statement. The occurrence of 16S RMTase genes in A. baumannii in the UK and Republic of Ireland is currently unknown. Aim. To identify the occurrence of 16S RMTase genes in A. baumannii isolates from the UK and the Republic of Ireland between 2004 and 2015. Methodology. Five hundred and fifty pan-aminoglycoside-resistant A. baumannii isolates isolated from the UK and the Republic of Ireland between 2004 and 2015 were screened by PCR to detect known 16S RMTase genes, and then whole-genome sequencing was conducted to screen for novel 16S RMTase genes. Results. A total of 96.5 % (531/550) of isolates were positive for 16S RMTase genes, with all but 1 harbouring armA (99.8 %, 530/531). The remaining isolates harboured rmtE3 , a new rmtE variant. Most (89.2 %, 473/530) armA -positive isolates belonged to international clone II (ST2), and the rmtE3 -positive isolate belonged to ST79. rmtE3 shared a similar genetic environment to rmtE2 but lacked an IS CR20 element found upstream of rmtE2 . Conclusion. This is the first report of rmtE in A. baumannii in Europe; the potential for transmission of rmtE3 to other bacterial species requires further research.