Determinants of beta-lactam resistance in meningitis-causing Enterobacteriaceae in Brazil

A set of antibiotic-resistance mechanisms and virulence factors in GES-16-producing Klebsiella quasipneumoniae subsp. similipneumoniae from hospital wastewater revealed by whole-genome sequencing

Klebsiella quasipneumoniae subsp. similipneumoniae has emerged as a human pathogen and sporadic isolates from non-clinical sources were reported. Here, we described the phenotypic- and genomic-characteristics of a multidrug-resistant (MDR) and potentially hypervirulent (MDR-hv) Klebsiella quasipneumoniae subsp. similipneumoniae (KqA1) isolated from hospital wastewater. The antibiotic susceptibility profile of KqA1 was investigated using disk-diffusion method, broth microdilution method, and agar dilution method, and the genetic characteristics of antimicrobial resistance, mobile genetics elements, and virulence were evaluated by genomic DNA sequencing on the Illumina® NovaSeq6000 platform as well as by bioinformatic analysis. Resistome analyses revealed the presence of genes related to resistance to β-lactams, aminoglycosides, quinolones, tetracyclines, sulfonamides, trimethoprim, chloramphenicol, macrolides, and fosfomycin. New genetic contexts to bla_GES-16 (carbapenemase gene) and to fosA (fosfomycin resistance gene) were described. A set of mechanisms that can contribute to antibiotic resistance, commonly detected in Klebsiella spp., was also found including chromosomal mutations, efflux systems, proteins, and regulators. Moreover, KqA1 presented genes related to tolerance to metals (arsenic, copper, nickel, cobalt, magnesium, cadmium, zinc, tellurium, selenium) and to biocides (quaternary-ammonium compounds). The isolate was classified as potentially hypervirulent due to a wide range of virulence factors found associated to regulation, motility, biofilm, effector delivery systems, immune modulation, nutritional/metabolic factors, adherence, invasion, and competitive advantage. The occurrence of MDR-hv KqA1 in hospital wastewater points out how this environment matrix plays a crucial role in the maintenance and selection of critical bacterial pathogens. Regarding One Health perspective, it is evident the need for multidisciplinary implementation of control measures for antibiotic-resistant bacteria, not only in hospital settings but also in a general environmental context to mitigate the dissemination of MDR and hv bacteria.

Extensively drug-resistant IMP-16-producing Pseudomonas monteilii isolated from cerebrospinal fluid

IMP-1-producing Pseudomonas aeruginosa was first reported in Japan and since then, bacteria with this metallo-β-lactamase have been detected worldwide. Pseudomonas monteilii (part of P. putida group) were considered an environmental pathogen with low virulence potential; however, multidrug-resistant and carbapenem-resistant P. monteilii have emerged. The present study reports the draft sequence of an extensively drug-resistant IMP-16-producing P. monteilii 597/14 isolated from cerebrospinal fluid in 2014. The sequencing data revealed blaIMP-16 as a gene cassette on class 1 integron, In1738 characterized in this study. Furthermore, the resistome of Pm597/14 consisted of 7 resistance genes (aadA1b, strA, strB, aacA4, blaIMP-16, blaOXA-2, sul1) and diverse virulence determinants involved in the adherence, LPS, antiphagocytosis, iron uptake and mercuric resistance. Although different virulence determinants were found in this study, using Galleria mellonella infection model, Pm597/14 did not kill any larvae between 7 days post-infection. P. monteilii isolates have been reported from clinical and environmental sources, carrying different MBL genes showing its potential role as their reservoir.

Dissemination of Klebsiella pneumoniae ST11 isolates with carbapenem resistance in integrated and emergency intensive care units in a Chinese tertiary hospital

PURPOSE

The aim of the present study was to investigate the dissemination of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates in integrated intensive care units (IICUs) and emergency ICUs (EICUs) for controlling the spread of CRKP in different ICUs of the hospital.

METHODOLOGY

From January 2016 to April 2017, a total of 46 non-duplicate CRKP isolates were consecutively isolated from a tertiary hospital. The production of carbapenemases was determined by the modified carbapenem inactivation method (mCIM) test. The resistance and virulence-associated genes were detected by PCR and DNA sequencing. A hypermucoviscosity phenotype was identified by the string test. Bacterial clonal relatedness of the CRKP isolates tested was determined by multi-locus sequence typing (MLST) and PFGE.

RESULTS

All CRKP isolates showed multiple drug resistance. All CRKP isolates harboured blaKPC-2-encoding carbapenemase and at least one of the other β-lactamase genes tested, with positive rates of 89.1  % (41/46) for blaCTX-M-65. qnrS was found among 76.1  % (35/46) of the CRKP isolates. A hypermucoviscosity phenotype was found in only two (4.3 %, 2/46) CRKP isolates. The virulence-associated genes with positive rates of more than 90  % among the 46 isolates tested included wabG (100 %, 46/46), ycf (100 %, 46/46), ureA (95.6 %, 44/46) and fim H (95.6 %, 44/46). MLST results showed that 46 CRKP isolates belonged to ST11 (95.6 %, 44/46) and ST86 (4.4 %, 2/46). PFGE patterns showed four clusters.

CONCLUSION

The CRKP ST11 clone with co-production of CTX-M-65 and KPC-2 disseminated in ICUs of this tertiary teaching hospital in central China. The emergence of CRKP with a hypermucoviscosity phenotype in ICUs should be of particular concern.

Extended-spectrum Beta-lactamase-producing Escherichia coli Meningitis That Developed from Otitis Media with Cholesteatoma

A 78-year-old man had a fever and exhibited disordered consciousness, which led to his transportation to our hospital. On arrival, he exhibited discharge from the ear. Because extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli was detected in the ear discharge and cerebrospinal fluid specimens, it was inferred to be the causal bacteria. Pulsed-field gel electrophoresis indicated the same ESBL-producing E. coli pattern in the patient's ear discharge, external auditory canal granulation, cerebrospinal fluid, and stool, indicating their common molecular epidemiological origin. Although ESBL-producing E. coli is an extremely rare cause of bacterial meningitis, it should be considered as a potential causal bacteria for community-acquired meningitis.

Virulence genes, capsular and plasmid types of multidrug-resistant CTX-M(-2, -8, -15) and KPC-2-producing Klebsiella pneumoniae isolates from four major hospitals in Brazil

We performed a single-month snapshot study of the population diversity of multidrug resistant (MDR) Klebsiella pneumoniae isolates producing carbapenemases and/or extended-spectrum β-lactamases from four major hospitals in Brazil. Isolates produced diverse ESBL (CTX-M-2, -8, -15, SHV-2), KPC-2 or both (CTX-M-2 and KPC-2), linked to specific genetic backgrounds and plasmids from a few families (IncR, IncFIIk, IncL/M) that were shared among clonal lineages within and between hospitals. A high clonal diversity was identified, among isolates from the same ST (ST11, ST15, ST101 or ST340). Diverse capsular types (n=13 K-types) were identified, most of which linked to specific ST (ST11 and K27 or K64, ST101 and K17, ST340 and KL151, ST15 and K24 or ST17 and KL112). Isolates shared a common set of virulence genes (ureA, fimH, uge, wabG, mrkD, entB) and occasionally ybtS (42%) and kfuBC (18%). Our data suggest intra- and inter-hospital spread of common genetic structures and international MDR K. pneumoniae clones.

Antimicrobial resistance and plasmid replicons in Yersinia enterocolitica strains isolated in Brazil in 30 years

Some studies evaluated the resistance profile of the Y. enterocolitica strains isolated in diverse countries. However, in Brazil the isolation and the study of Y. enterocolitica are not common and therefore information about the antimicrobial resistance profile of this species in this country is scarce. Therefore, the aim of this study was to evaluate the antimicrobial resistance of Y. enterocolitica of biotypes 1A, 2 and 4 isolated from clinical and non-clinical sources between 1979 and 2012, in Brazil. This study showed that some Yersinia enterocolitica of different biotypes remain susceptible to antimicrobials used for gastroenteritis treatment. Moreover, neither acquired resistance genes nor diversity of plasmids replicons were found; however, variation in the in vitro intrinsic resistant pattern was detected, except the non-resistance to cefoxitin in all strains. Notwithstanding, due to epidemiological link between Y. enterocolitica and the pork production chain, monitoring plasmid acquired resistance in Y. enterocolitica could also be considered for antimicrobial resistance control purposes and food safety measures.

Virulence and Genomic Feature of a Virulent Klebsiella pneumoniae Sequence Type 14 Strain of Serotype K2 Harboring blaNDM-5 in China

The objective of this study was to reveal the molecular mechanism involved in carbapenem resistance and virulence of a K2 Klebsiella pneumoniae clinical isolate 24835. The virulence of the strain was determined by in vitro and in vivo methods. The de novo whole-genome sequencing technology and molecular biology methods were used to analyze the genomic features associated with the carbapenem resistance and virulence of K. pneumoniae 24835. Strain 24835 was highly resistant to carbapenems and belonged to ST14, exhibited hypermucoviscous and unique K2-aerobactin-kfu-rmpA positive phenotype. As the only carbapenemase gene in strain 24835, bla_NDM–5 was located on a 46-kb IncX3 self-transmissible plasmid, which is a very close relation of pNDM-MGR194 from India. Genetic context of bla_NDM–5 in strain 24835 was closely related to those on IncX3 plasmids in various Enterobacteriaceae species in China. The combination of multiple virulence genes may work together to confer the relative higher virulence in K. pneumoniae 24835. Significantly increased resistance to serum killing and mice mortality were found in the virulent New Delhi metallo-β-lactamase (NDM)-producing K. pneumoniae strain compared to the other NDM-producing K. pneumoniae strain. Our study provides basic information of phenotypic and genomic features of K. pneumoniae 24835, a strain displaying carbapenem resistance and relatively high level of virulence. These findings are concerning for the potential of NDM-like genes to disseminate among virulent K. pneumoniae isolates.

Antimicrobial resistance in Enterobacteriaceae in Brazil: focus on β-lactams and polymyxins

During the last 30 years there has been a dissemination of plasmid-mediated β-lactamases in Enterobacteriaceae in Brazil. Extended spectrum β-lactamases (ESBL) are widely disseminated in the hospital setting and are detected in a lower frequency in the community setting. Cefotaximases are the most frequently detected ESBL type and Klebsiella pneumoniae is the predominant species among ESBL producers. Klebsiella pneumoniae carbapenemase-producing Enterobacteriaceae became widely disseminated in Brazil during the last decade and KPC production is currently the most frequent resistance mechanism (96.2%) in carbapenem resistant K. pneumoniae. To date KPC-2 is the only variant reported in Brazil. Polymyxin B resistance in KPC-2-producing K. pneumoniae has come to an alarming rate of 27.1% in 2015 in São Paulo, the largest city in Brazil. New Delhi metallo-β-lactamase was detected in Brazil in 2013, has been reported in different Brazilian states but are not widely disseminated. Antimicrobial resistance in Enterobacteriaceae in Brazil is a very serious problem that needs urgent actions which includes both more strict adherence to infection control measures and more judicious use of antimicrobials.

First Report of Complete Sequence of a blaNDM-13-Harboring Plasmid from an Escherichia coli ST5138 Clinical Isolate

Since the first report of bla_NDM-1, 16 bla_NDM variants have been identified among Gram-negative bacteria worldwide. Recently, a novel bla_NDM variant, bla_NDM-13, was identified in the chromosome of an ST101 Escherichia coli isolate from Nepal. Here we first reported plasmid-mediated bla_NDM-13 in a carbapenem-resistant E. coli ST5138 clinical isolate associated with hospital-acquired urinary tract infection from China. bla_NDM-13 and bla_SHV-12 coexisted on the a ~54 Kb self-transferable plasmid. Compared with NDM-1, NDM-13, NDM-3, and NDM-4 had two amino acid substitutions (D95N and M154L), one amino acid substitution (D95N) and one amino acid substitutions (M154L), respectively. Complete plasmid sequencing showed that bla_NDM-13-harboring plasmid (pNDM13-DC33) was highly similar to the bla_NDM-1-harboring IncX3 plasmid pNDM-HN380, a common bla_NDM-harboring vector circulating in China. In accordance with the structure of pNDM-HN380, pNDM13-DC33 consists of a 33-kb backbone encoding plasmid replication (repB), stability partitioning, and transfer (tra, trb, and pil) functions, and a 21-kb antimicrobial resistance region with high GC content between umuD and mpr genes. In conclusion, the present study is the first report of a plasmid-encoded bla_NDM-13 and the complete sequence of a bla_NDM-13-harboring plasmid (pNDM13-DC33). bla_NDM-13 maybe originate from bla_NDM-1 located on a pNDM-HN380-like plasmid by sequential mutations.

Outbreak by Ventilator-Associated ST11 K. pneumoniae with Co-production of CTX-M-24 and KPC-2 in a SICU of a Tertiary Teaching Hospital in Central China

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) often responsible for numerous hospital-associated outbreaks has become an important public health problem. From January 2013 to February 2014, a total of 41 non-duplicate K. pneumoniae isolates with carbapenem resistance, were collected at a tertiary teaching hospital in Nanchang, central China. Among 41 K. pneumoniae isolates, 28 were isolated from hospitalized patients including 19 from the patients in surgery intensive care unit (SICU) and 13 were isolated from ventilators. Twenty-four of 28 patients infected by CRKP have been submitted to mechanical ventilation using ventilator. More than 95% of the CRKP isolates were resistant to 13 antimicrobials tested. All CRKP isolates were confirmed as carbapenemase producer and were positive for bla KPC-2, with one positive for both blaKPC-2 and bla NDM-1. All carbapenemase-producing isolates harbored at least one of extended spectrum β-lactamase genes tested, among which 95.1% (39/41) of the tested isolates were found to harbor both bla CTX-M-24 and bla KPC-2, Of note, one isolate harbored simultaneously two carbapenemase genes (bla KPC-2 and bla NDM-1) and two ESBL genes (bla CTX-M-3 and bla TEM-104). To the best of our knowledge, coexistence of bla KPC-2 and bla CTX-M-24 in one isolate is first reported. MLST results showed that 41 CRKP isolates belonged to four sequence types (STs) including ST11, novel ST1854, novel ST1855, and ST1224. PFGE results displayed three PFGE clusters. Thirty-eight ST11 CRKP isolates (92.7%, 38/41) including all 13 isolates from ventilators and 25 isolates from patients from seven wards (18 from SICU) belonged to same PFGE cluster, indicating these isolates were clonally related. Fifteen isolates have an identical undistinguished pattern (100% similarity) forming a single clonal population. Moreover, this clone was exclusively linked to the cases attended in SICU and linked to the Ventilators. Additionally, the other SICU cases were linked to closely related clones (similarity greater than 95%). These data indicated that the occurrence of a clonal outbreak associated with ventilators has been found. In conclusion, outbreak by ventilator-associated ST11 K. pneumoniae with co-production of CTX-M-24 and KPC-2 is found in a SICU of a tertiary teaching hospital in central China.

Detection of blaCTX-M-type genes in complex class 1 integrons carried by Enterobacteriaceae isolated from retail chicken meat in Brazil

CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae have been increasingly identified in humans and animals, and their potential transmission by contaminated food has been highlighted. In this study, we report for the first time the isolation of multidrug-resistant (MDR) Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis strains harboring blaCTXM-2 or blaCTXM-8 gene variants in chicken meat sold in markets in southeast Brazil. In this regard, the genetic environment of the blaCTX-M-2 gene is composed of a complex class 1 integron and an ISCR1-associated sequence with dfr and/or aadA gene cassettes located within the variable region. In summary, chicken meat may be a reservoir of MDR Enterobacteriaceae harboring blaCTX-M-type genes, which is a public health concern.

Expansion and evolution of a virulent, extensively drug-resistant (polymyxin B-resistant), QnrS1-, CTX-M-2-, and KPC-2-producing Klebsiella pneumoniae ST11 international high-risk clone

In this study, we report the early expansion, evolution, and characterization of a multiresistant Klebsiella pneumoniae clone that was isolated with increasing frequency from inpatients in a tertiary-care university hospital in Brazil. Seven carbapenem- and quinolone-resistant and polymyxin B-susceptible or -resistant K. pneumoniae isolates isolated between December 2012 and February 2013 were investigated. Beta-lactamase- and plasmid-mediated quinolone resistance (PMQR)-encoding genes and the genetic environment were investigated using PCR, sequencing, and restriction fragment length polymorphism (RFLP). Clonal relatedness was established using XbaI-pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and phylogenetic group characterization. Plasmid analyses included PCR-based replicon typing (PBRT) and hybridization of the S1-PFGE product, plasmid MLST, and conjugation experiments. Virulence potential was assessed by PCR by searching for 10 virulence factor-encoding genes (ureA, fimH, kfuBC, uge, wabG, magA, mrkD, allS, rmpA, and cf29a) and by phenotypic tests to analyze the hypermucoviscous phenotype. The genetic context of a multidrug-resistant and extensively drug-resistant K. pneumoniae ST11-KpI clone harboring IncFIIk-Tn4401a-blaKPC-2, qnrS1, and blaCTX-M-2 was found. Moreover, three isolates displayed high resistance to polymyxin B (MICs = 32, 32, and 128 mg/liter) as well as mucous and hypermucoviscous phenotypes. These bacteria also harbored ureA, fimH, uge, wabG, and mrkD, which code for virulence factors associated with binding, biofilm formation, and the ability to colonize and escape from phagocytosis. Our study describes the association of important coresistance and virulence factors in the K. pneumoniae ST11 international high-risk clone, which makes this pathogen successful at infections and points to the quick expansion and evolution of this multiresistant and virulent clone, leading to a pandrug-resistant phenotype and persistent bacteria in a Brazilian hospital.

Distribution of strain type and antimicrobial susceptibility of Escherichia coli isolates causing meningitis in a large urban setting in Brazil

The clinical management of meningitis caused by Escherichia coli is greatly complicated when the organism becomes resistant to broad-spectrum antibiotics. We sought to characterize the antimicrobial susceptibilities, sequence types (ST), and presence of known drug resistance genes of E. coli isolates that caused meningitis between 1996 and 2011 in Salvador, Brazil. We then compared these findings to those for E. coli isolates from community-acquired urinary tract infections (UTI) that occurred during the same time period and in the same city. We found that 19% of E. coli isolates from cases of meningitis and less than 1% of isolates from UTI were resistant to third-generation cephalosporins. The sequence types of E. coli isolates from cases of meningitis included ST131, ST69, ST405, and ST62, which were also found among isolates from UTI. Additionally, among the E. coli isolates that were resistant to third-generation cephalosporins, we found genes that encode the extended-spectrum beta-lactamases CTX-M-2, CTX-M-14, and CTX-M-15. These observations demonstrate that compared to E. coli strains isolated from cases of community-acquired UTI, those isolated from cases of meningitis are more resistant to third-generation cephalosporins, even though the same sequence types are shared between the two forms of extraintestinal infections.

[Case of an elderly patient with community acquired bacterial meningitis due to extended spectrum β lactamase producing Escherichia coli]

Community acquired bacterial meningitis due to extended spectrum β lactamase-producing Escherichia coli is very rare. We report the case of a 72-year-old woman being treated for longstanding diabetes mellitus. She developed lower back pain accompanied by elevated body temperature, and was transported to the emergency unit in our hospital five days later because of impaired consciousness. An abdominal plane CT showed acute pyelonephritis and a brain MRI showed inflammatory exudate in the posterior horn of her bilateral ventricles. A lumbar puncture was performed, and examination of the cerebrospinal fluid revealed a marked elevation in her cell count (polymorphonuclear leukocytes dominant) that we diagnosed as bacterial meningitis. Initially, she was treated with intravenous meropenem, ceftriaxon, and vancomycin. Extended spectrum β lactamase-producing Escherichia coli were then detected in her urinary and blood cultures, and the antibiotics were changed to intravenous meropenem, gentamicin, and intrathecal gentamicin. Her clinical symptoms improved, but her inflammatory reaction was prolonged and we detected spondylitis. She was then treated with levofloxacin, and the inflammatory reaction improved. Extended spectrum β lactamase-producing Escherichia coli should be taken into consideration as a cause of community acquired bacterial meningitis.

Dissemination of blaKPC-2 by the spread of Klebsiella pneumoniae clonal complex 258 clones (ST258, ST11, ST437) and plasmids (IncFII, IncN, IncL/M) among Enterobacteriaceae species in Brazil

This article reports the spread of bla(KPC-2) in the Sao Paulo and Rio de Janeiro states, facilitated by globally spread K. pneumoniae clonal complex 258 (CC258) clones (ST258, ST11, and ST437) and a diversity of plasmids (IncFII, IncN, and IncL/M, two untypeable plasmids carrying Tn4401a or Tn4401b) successfully disseminated among species of the Enterobacteriaceae (Enterobacter cloacae, Serratia marcescens, and Citrobacter freundii). It also constitutes the first description of sequence type 258 (ST258) in Brazil, which was associated with a nosocomial hospital outbreak in Ribeirao Preto city.