Emergence and Polyclonal Dissemination of OXA-244–Producing Escherichia coli,France

Since 2016, OXA-244–producing Escherichia coli has been increasingly isolated in France. We sequenced 97 OXA-244–producing E. coli isolates and found a wide diversity of sequence types and a high prevalence of sequence type 38. Long-read sequencing demonstrated the chromosomal location of bla_OXA-244 inside the entire or truncated Tn51098.     

Clonal complexes 104, 109 and 113 playing a major role in the dissemination of OXA-carbapenemase-producing Acinetobacter baumannii in Southeast Brazil

Carbapenem resistance among Acinetobacter baumannii strains isolated from clinical settings in Brazil has increased dramatically in the last 10 years due to the emergence and dissemination of OXA-type carbapenemase encoding genes. This study aimed to characterize the presence of carbapenem-hydrolyzing class D β-lactamases (CHDL)-encoding genes and clonal complexes playing a major role in the dissemination of OXA-carbapenemase-producing A. baumannii in Southeast Brazil.A total of 74 A. baumannii strains isolated from patients admitted to 4 hospitals in Southeast Brazil were analyzed. Molecular characterization of strains revealed that 67 strains carried bla_OXA-23 (72%), bla_OXA-143 (25%) or both genes (3%). PFGE analysis identified 12 PFGE clusters, grouping 26 pulsotypes. Two PFGE clusters were predominant, comprising more than 66% of OXA-producing A. baumannii isolates. Among 23 representative strains characterized by MLST-UO (Multilocus Sequence Typing Scheme – University of Oxford, http://pubmlst.org/abaumannii/), 14 different STs were identified, of which six were confirmed as novel sequence types (designated as STs 402–407). Most of these isolates belonged to clonal complexes CC104,CC109 or CC113, whereas three STs were singletons (ST339, 403 and 407).In conclusion, the presence of bla_OXA-23- and bla_OXA-143-like genes was not related to specific ST/CC, suggesting that the dissemination of OXA-carbapenemase-encoding genes may involve different STs, in which the spread of OXA-23-like is most likely due to mobile elements (i.e., plasmids). In this regard, CC104, CC109 and CC113 played a major role as predominant CDHL-carrying clones, instead of CC92, which was not identified.     

Phylogenetic analysis of carbapenem-resistant Acinetobacter baumannii isolated from different sources using Multilocus Sequence Typing Scheme

The emergence and worldwide distribution of carbapenem-resistant Acinetobacter baumannii strains has become a major public health threat. The objective of this study was to investigate the clonal relatedness of A. baumannii isolates collected from clinical and extra-hospital environments in Mthatha, South Africa. Forty carbapenem-resistant isolates comprising of clinical (20) and extra-hospital (20) were identified and tested for antimicrobial susceptibility. Detection of carbapenemase encoding genes was performed by Real-time PCR. The clonal relationship of clinical isolates relative to extra-hospital isolates was determined via multilocus sequence typing (MLST). All isolates (clinical and extra-hospital) were resistant to most common antibiotics including carbapenems (imipenem; MIC ≥32 μg/mL and meropenem; MIC ≥32 μg/mL) with the only exception being amikacin (with 3 isolates susceptible), tigecycline (14 isolates susceptible) and colistin (all isolates susceptible). The bla OXA-23-like and the intrinsic bla OXA-51 -like genes were detected in all the isolates tested. The bla OXA-58-like and bla IMP-type genes were detected in 2 clinical isolates whilst the bla OXA-24-like, bla VIM-type, bla NDM-1, bla SIM, and bla AmpC were not detected. The bla OXA-24-like, bla OXA-58-like, bla IMP-type, bla VIM-type, bla NDM-1, bla SIM, and bla AmpC were negative in the extra-hospital isolates. Co-occurrence of bla OXA-23 -like, bla OXA-58-like and bla IMP-type was observed in 2 clinical isolates. The MLST performed on 33 isolates identified 5 existing sequence types (ST) (ST1, ST2, ST25, ST85 and ST215) in clinical isolates and 2 existing STs (ST1 and ST2) in extra-hospital isolates. The most dominant ST was ST2 accounting for 68.8% of the clinical isolates and 82.4% of the extra-hospital isolates. The study demonstrated high prevalence and potential clonal spread of globally-disseminated clonal complex 2 carrying bla OXA-23-like within our local settings. However, ST25 might be an emerging lineage carrying the bla OXA-23-like . Continuous monitoring is important in limiting the spread of these strains in other healthcare settings and the community.     

A reliable combination method to identification and typing of epidemic and endemic clones among clinical isolates of Acinetobacter baumannii

The multi-drug resistant (MDR) Acinetobacter baumannii as an important nosocomial pathogen has emerged a global health concern in recent years. In this study, we applied three easier, faster, and cost-effective methods including PCR-based open reading frames (ORFs) typing, sequence typing of bla_OXA-51-like and RAPD-PCR method to rapid typing of A. baumannii strains. Taken together in the present study the results of ORFs typing, PCR-sequencing of bla_OXA-51-like genes and MLST sequence typing revealed there was a high prevalence (62%, 35/57) of ST2 as international and successful clone which detected among clinical isolates of multi-drug resistant A. baumannii with ORF pattern B and bla_OXA-66 gene. Only 7% (4/57) of MDR isolates belonged to ST1 with ORF pattern A and bla_OXA-69 gene. Interestingly, we detected singleton ST513 (32%, 18/57) that encoded bla_OXA-90 and showed the ORF pattern H as previously isolated in Middle East. Moreover, our data showed RAPD-PCR method can detect divergent strains of the STs. The Cl-1, Cl-2, Cl-3, Cl-4, Cl-10, Cl-11, Cl-12, Cl-13 and Cl-14 belonged to ST2. While the Cl-6, Cl-7, Cl-8 and Cl-9 belonged to ST513. Only Cl-5 belonged to ST1. It seems that the combination of these methods have more discriminatory than any method separately and could be effectively applied to rapid detection of the clonal complex (CC) of A. baumannii strains without performing of MLST or PFGE.     

Outbreak of IncX8 Plasmid–Mediated KPC-3–Producing Enterobacterales Infection,China

Carbapenem-resistant Enterobacterales (CRE) infection is highly endemic in China; Klebsiella pneumoniae carbapenemase (KPC) 2–producing CRE is the most common, whereas KPC-3–producing CRE is rare. We report an outbreak of KPC-3–producing Enterobacterales infection in China. During August 2020–June 2021, 25 bla_KPC-3–positive Enterobacteriale isolates were detected from 24 patients in China. Whole-genome sequencing analysis revealed that the bla_KPC-3 genes were harbored by IncX8 plasmids. The outbreak involved clonal expansion of KPC-3–producing Serratia marcescens and transmission of bla_KPC-3 plasmids across different species. The bla_KPC-3 plasmids demonstrated high conjugation frequencies (10⁻³ to 10⁻⁴). A Galleria mellonella infection model showed that 2 sequence type 65 K2 K. pneumoniae strains containing bla_KPC-3 plasmids were highly virulent. A ceftazidime/avibactam in vitro selection assay indicated that the KPC-3–producing strains can readily develop resistance. The spread of bla_KPC-3–harboring IncX8 plasmids and these KPC-3 strains should be closely monitored in China and globally.     

Emergence and spread of carbapenem-resistant Acinetobacter baumannii sequence type 191 in a Korean hospital

Emergence and spread of specific carbapenem-resistant Acinetobacter baumannii (CRAB) clones cause a serious therapeutic problem. This study was aimed to investigate the clonal diversity and genetic basis of antimicrobial resistance among the 69 CRAB isolates from 2009 to 2010 in a Korean hospital. All CRAB isolates were found to be sequence type (ST) 2 using the Institute Pasteur’s multilocus sequence typing (MLST) scheme, but classified into two sequence groups and nine pulsotypes. Fifty-six CRAB isolates belonging to two main pulsotypes were found to be ST191 using the Bartual’s MLST scheme. All CRAB isolates showed an extensively drug-resistant phenotype. The bla_OXA-51/bla_OXA-23, bla_AmpC/bla_PER-1 and armA genes were largely responsible for resistance to carbapenems, extended-spectrum β-lactams and aminoglycosides, respectively. The first CRAB strains identified in 2005 in this hospital were found to be ST2 using the Institute Pasteur’s MLST scheme, but showed ST353 using the Bartual’s MLST scheme and different pulsotypes from the CRAB isolates from 2009 to 2010. In conclusion, this is the first report of emergence and spread of A. baumannii ST191 in Korea, as well of the genetic basis of its antimicrobial resistance.     

Nosocomial spread of carbapenem-resistant Acinetobacter baumannii (types ST75 and ST137) carrying blaOXA-23-like gene with an upstream ISAba1 in a Chinese hospital

The most widespread type of carbapenemases among carbapenem-resistant Acinetobacter baumannii (CRAB) belongs to the oxacillinase (OXA) group. A total of 57 CRAB isolates and 20 non-CRAB isolates (i.e., A. baumannii susceptible to carbapenems) were studied to investigate the molecular epidemiology of CRAB isolates and to identify the OXAs responsible for resistance to imipenem. The ISAba1-bla_OXA-23-like gene was detected in all 57 CRAB isolates but was detected in none of the non-CRAB isolates. Pulsed-field gel electrophoresis (PFGE) revealed that clones A and B were the dominant genotypes, and all bla_OXA-23-like gene positive strains were classified as either clone A or B strains. ST75 and ST137 were the most prominent sequence types (STs). Finally, the A. baumannii isolates of clone A, C and F were all demonstrated to be genetically similar to the previously identified European clone II. In conclusion, ST75- and ST137-type CRAB isolates that produced the bla_OXA-23-like gene with an upstream ISAba1 contributed to the nosocomial outbreaks studied in this work.     

Genomic Epidemiology of Global Carbapenemase-Producing Escherichia coli, 2015–2017

We describe the global molecular epidemiology of 229 carbapenemase-producing Escherichia coli in 36 countries during 2015–2017. Common carbapenemases were oxacillinase (OXA) 181 (23%), New Delhi metallo-β-lactamase (NDM) 5 (20%), OXA-48 (17%), Klebsiella pneumoniae carbapenemase 2 (15%), and NDM-1 (10%). We identified 5 dominant sequence types (STs); 4 were global (ST410, ST131, ST167, and ST405), and 1 (ST1284) was limited to Turkey. OXA-181 was frequent in Jordan (because of the ST410-B4/H24RxC subclade) and Turkey (because of ST1284). We found nearly identical IncX3-bla_OXA-181 plasmids among 11 STs from 12 countries. NDM-5 was frequent in Egypt, Thailand (linked with ST410-B4/H24RxC and ST167-B subclades), and Vietnam (because of ST448). OXA-48 was common in Turkey (linked with ST11260). Global K. pneumoniae carbapenemases were linked with ST131 C1/H30 subclade and NDM-1 with various STs. The global carbapenemase E. coli population is dominated by diverse STs with different characteristics and varied geographic distributions, requiring ongoing genomic surveillance.     

Phylogeny and Disease Association of Shiga Toxin�Cproducing Escherichia coli O91

The diversity and relatedness of 100 Shiga toxin–producing Escherichia coli O91 isolates from different patients were examined by multilocus sequence typing. We identified 10 specific sequence types (ST) and 4 distinct clonal groups. ST442 was significantly associated with hemolytic uremic syndrome.     

Genomic Characterization of hlyF-positive Shiga Toxin–Producing Escherichia coli,Italy and the Netherlands, 2000–2019

Shiga toxin–producing Escherichia coli (STEC) O80:H2 has emerged in Europe as a cause of hemolytic uremic syndrome associated with bacteremia. STEC O80:H2 harbors the mosaic plasmid pR444_A, which combines several virulence genes, including hlyF and antimicrobial resistance genes. pR444_A is found in some extraintestinal pathogenic E. coli (ExPEC) strains. We identified and characterized 53 STEC strains with ExPEC-associated virulence genes isolated in Italy and the Netherlands during 2000–2019. The isolates belong to 2 major populations: 1 belongs to sequence type 301 and harbors diverse stx₂ subtypes, the intimin variant eae-ξ, and pO157-like and pR444_A plasmids; 1 consists of strains belonging to various sequence types, some of which lack the pO157 plasmid, the locus of enterocyte effacement, and the antimicrobial resistance–encoding region. Our results showed that STEC strains harboring ExPEC-associated virulence genes can include multiple serotypes and that the pR444_A plasmid can be acquired and mobilized by STEC strains.     

Evolutionary dynamics of carbapenem-resistant Acinetobacter baumannii circulating in Chilean hospitals

We analyze the evolutionary dynamics of ninety carbapenem-resistant Acinetobacter baumannii (CRAB) isolates collected between 1990 and 2015 in Chile. CRAB were identified at first in an isolate collected in 2005, which harbored the ISAba1-bla_OXA-69 arrangement. Later, OXA-58- and OXA-23-producing A. baumannii strains emerged in 2007 and 2009, respectively. This phenomenon was associated with variations in the epidemiology of OXA-type carbapenemases, linked to nosocomial lineages belonging to ST109, ST162, ST15 (CC15) and ST318 (CC15).     

Molecular Typing and Epidemiology of Human Listeriosis Cases,Denmark, 2002–2012

Denmark has a high incidence of invasive listeriosis (0.9 cases/100,000 population in 2012). We analyzed patient data, clinical outcome, and trends in pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) of Listeria monocytogenes strains isolated in Denmark during 2002–2012. We performed 2-enzyme PFGE and serotyping on 559 isolates and MLST on 92 isolates and identified some correlation between molecular type and clinical outcome and patient characteristics. We found 178 different PFGE types, but isolates from 122 cases belonged to just 2 closely related PFGE types, clonal complex 8 and sequence type 8. These 2 types were the main cause of a peak in incidence of invasive listeriosis during 2005–2009, possibly representing an outbreak or the presence of a highly prevalent clone. However, current typing methods could not fully confirm these possibilities, highlighting the need for more refined discriminatory typing methods to identify outbreaks within frequently occurring L. monocytogenes PFGE types.     

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

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

Multicentre investigation of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in Bulgarian hospitals – Interregional spread of ST11 NDM-1-producing K. pneumoniae

AimThe aim of this study was to investigate the mechanisms of beta-lactam-resistance and the clonal relatedness of carbapenem-nonsusceptible Klebsiella pneumoniae and Escherichia coli isolates, collected consecutively in eight centers in five Bulgarian cities from November 2014 to March 2018. Carbapenemase-producing enterobacteria were detected in all but one centers. Overall, 104 K. pneumoniae and one E. coli were analysed.Materials and methodsAntimicrobial susceptibility and beta-lactamases were analysed. Conjugation experiments, plasmid fingerprinting and replicon typing, as well as MLST and ERIC-PCR were carried out.ResultsKPC-2 (51%) and NDM-1 (47%) were the main carbapenemases identified. KPC-2 producing K. pneumoniae were classified into 10 MLST-types. The four dominating MLST-types ST29, ST15, ST336 and ST902 comprised 79% of the KPC-2 producers. All but one of the NDM-1 producing isolates belonged to the MLST-type ST11 and were found in seven centers. Furthermore, single K. pneumoniae isolates producing VIM-1 (ST147) and OXA-48 (ST15) were identified. In addition to the carbapenemases, the ESBLs CTX-M-15, CTX-M-3, and SHV-12 as well as AmpC enzyme CMY-4 were found. The FIIAs-replicon-type was found in all KPC-2 producers while the A/C-replicons dominated in NDM-1 producing isolates. The single NDM-1 producing E. coli was determined as MLST-Type ST10 (Warwick scheme).ConclusionThe interregional clonal expansion of NDM-1 producing ST11 K. pneumoniae and the dissemination of bla_KPC-2 carrying plasmids were responsible for the spread of carbapenemase-producing K. pneumoniae in Bulgaria. Our findings highlight the urgency to prevent dissemination of these highly transmissible and dangerous lineages.     

Emergence of carbapenem resistant Escherichia coli isolates producing blaNDM and blaOXA-48-like carried on IncA/C and IncL/M plasmids at two Iranian university hospitals

The emergence of carbapenem resistance among Escherichia coli is a serious threat to public health. The objective of this study was to investigate resistance genes and clonality of carbapenem resistant E. coli in Iran. Between February 2015 and July 2016, a total of 32 non-duplicate E. coli isolates that were ertapenem resistant or intermediate (R/I-ETP) were collected from patient clinical or surveillance cultures (rectal swabs) at two university hospitals. Resistance genes were identified by PCR and sequencing. Conjugation experiments, PCR-based replicon typing, PFGE and multilocus sequence typing (MLST) were performed. PCR assays showed, among the 32 isolates, twenty-nine strains produced carbapenemase genes. The predominant carbapenemase was bla_OXA-48 (82.8%), followed by bla_NDM-1 (31%), bla_NDM-7 (6.9%) and bla_OXA-181 (3.4%). Seven of the bla_NDM positive isolates co-harbored bla_OXA-48 carbapenemases. The bla_NDM and bla_OXA-48 were found in IncA/C and IncL/M conjugative plasmids, respectively. The bla_CTX-M-15, qnrA and intI1 genes were also present in most isolates. The PFGE revealed genetic diversity among the 28 E. coli isolates, which belonged to six minor PFGE clusters and 14 isolates were singletons. The 26 isolates were distributed into 18 STs, of which two were dominant (ST648 and ST167). We identified one bla_NDM-1-positive ST131 E. coli isolates that harbor the bla_CTX-M-15 and bla_TEM genes. Horizontal transfer of IncA/C and IncL/M plasmids has likely facilitated the spread of the bla_OXA-48 and bla_NDM genes among E. coli. Their clonal diversity and the presence of faecal carriers in isolates suggest an endemic spread of OXA-48 and NDM. Therefore, it emphasizes the critical importance of monitoring and controlling the spread of carbapenem resistant E. coli.     

Genomic Epidemiology of Azithromycin-Nonsusceptible Neisseria gonorrhoeae,Argentina, 2005–2019

Azithromycin-nonsusceptible Neisseria gonorrhoeae strains are an emerging global public health threat. During 2015–2018, the prevalence of azithromycin-nonsusceptible gonococcal infection increased significantly in Argentina. To investigate the genomic epidemiology and resistance mechanisms of these strains, we sequenced 96 nonsusceptible isolates collected in Argentina during 2005–2019. Phylogenomic analysis revealed 2 main clades, which were characterized by a limited geographic distribution, circulating during January 2015–November 2019. These clades included the internationally spreading multilocus sequence types (STs) 1580 and 9363. The ST1580 isolates, which had MICs of 2–4 μg/mL, had mutations in the 23S rRNA. The ST9363 isolates, which had MICs of 2–4 or >256 μg/mL, had mutations in the 23S rRNA, a mosaic mtr locus, or both. Identifying the geographic dissemination and characteristics of these predominant clones will guide public health policies to control the spread of azithromycin-nonsusceptible N. gonorrhoeae in Argentina.     

鲍曼不动杆菌碳青霉烯酶基因型及分子流行病学研究

目的研究宁波地区3家综合性医院临床分离亚胺培南耐药鲍曼不动杆菌的耐药性、同源性及碳青霉烯酶基因型。方法收集宁波市李惠利医院、宁波市第一人民医院、宁波市第二人民医院碳青霉烯类抗生素耐药鲍曼不动杆菌28株。琼脂稀释法和E-test法测定14种抗菌药物的最小抑菌浓度值;脉冲场凝胶电泳（PFGE）分析菌株同源性;PCR及克隆测序分析碳青霉烯酶基因型。结果28株鲍曼不动杆菌对多粘菌素E耐药率最低为4．7%,头孢哌酮/舒巴坦为87%,其余抗菌药物耐药率均高于90%耐药。PFGE分型共分为4型,以A、B两型为主。28株鲍曼不动杆菌中均产OXA-23碳青霉烯酶基因,未检测到VIM、IMP型金属酶基因。结论宁波地区碳青霉烯抗生素耐药鲍曼不动杆菌均产OXA-23型碳青霉烯酶,3家医院均有克隆播散流行。     

Transfer of Carbapenem-Resistant Plasmid from Klebsiella pneumoniae ST258 to Escherichia coli in Patient

Klebsiella pneumoniae carbapenemase (KPC) 3–producing Escherichia coli was isolated from a carrier of KPC-3–producing K. pneumoniae. The KPC-3 plasmid was identical in isolates of both species. The patient''s gut flora contained a carbapenem-susceptible E. coli strain isogenic with the KPC-3–producing isolate, which suggests horizontal interspecies plasmid transfer.     

Outbreak of Panton-Valentine Leukocidin–Associated Methicillin-Susceptible Staphylococcus aureus Infection in a Rugby Team,France, 2010–2011

Staphylococcus aureus strains that produce Panton-Valentine leukocidin are known to cause community infections. We describe an outbreak of skin abscesses caused by Panton-Valentine leukocidin–producing methicillin-susceptible S. aureus (clonal complex 121) in a professional rugby team in France during July 2010–February 2011. Eight team members were carriers; 7 had skin abscesses.