A novel CTX-M beta-lactamase (CTX-M-8) in cefotaxime-resistant Enterobacteriaceae isolated in Brazil

Detection of Salmonella Mbandaka Carrying the blaCTX-M-8 Gene Located on IncI1 Plasmid Isolated from a Broiler Flock Environment

Salmonella Mbandaka is one of the most globally widespread serovars, occurring in many sources and included among twenty serovars that contribute to human salmonellosis in Europe. In Poland, it has been noted in non-human sources since 1996, being found firstly in feeds and later in waterfowl and chicken. Over the years, it gained epidemiological importance, being isolated from a wide range of animal species, including livestock. Generally, it is characterized by sensitivity to most antimicrobials and the ability to form biofilms. The occurrence of cephalosporin-resistant Salmonella in non-human sources is an extremely rare phenomenon in Poland. In this report, we characterized the full genome of the ESBL-producing S. Mbandaka strain isolated from a broiler farm environment (boot swab sample) in Poland in 2022. The isolate was serotyped as S. Mbandaka according to the White-Kaufmann-Le Minor scheme. Antimicrobial susceptibility testing performed with the microbroth dilution method showed its resistance to ampicillin, cefotaxime, ceftazidime, ciprofloxacin, and nalidixic acid. The whole-genome sequence was reconstructed using short and long reads and assembled into the complete chromosome and three plasmids: IncI1 pST113 (89,439 bp), Col(pHAD28) (2699 bp), and Col440 (2495 bp). The strain belonged to sequence type ST413. Plasmid analysis showed blaCTX-M-8 mobilization on IncI1(alpha) surrounded with insertion sequences. The analyzed genome content draws attention to the possibility of the horizontal spread of the resistance genes. To the best of our knowledge, this is the first report of blaCTX-M-8-positive Salmonella in Poland.

Emergence of a clinical Salmonella enterica serovar 1,4,[5], 12: i:-isolate, ST3606, in China with susceptibility decrease to ceftazidime-avibactam carrying a novel blaCTX-M-261 variant and a blaNDM-5

PURPOSE

The detection rate of Salmonella enterica serovar 1,4,[5], 12: i: - (S. 1,4,[5], 12: i: -) has increased as the most common serotype globally. A S. 1,4,[5], 12: i: - strain named ST3606 (sequence type 34), isolated from a fecal specimen of a child with acute diarrhea hospitalized in a tertiary hospital in China, was firstly reported to be resistant to carbapenem and ceftazidime-avibactam. The aim of this study was to characterize the whole-genome sequence of S. 1,4,[5], 12: i: - isolate, ST3606, and explore its antibiotic resistance genes and their genetic environments.

METHODS

The genomic DNA of S. 1,4,[5], 12: i: - ST3606 was extracted and performed with single-molecule real-time sequencing. Resistance genes, plasmid replicon type, mobile elements, and multilocus sequence types (STs) of ST3606 were identified by ResFinder 3.2, PlasmidFinder, OriTfinder database, ISfinder database, and MLST 2.0, respectively. The conjugation experiment was utilized to evaluate the conjugation frequency of pST3606-2. Protein expression and enzyme kinetics experiments of CTX-M were performed to analyze hydrolytic activity of a novel CTX-M-261 enzyme toward several antibiotics.

RESULTS

Single-molecule real-time sequencing revealed the coexistence of a 109-kb IncI1-Iα plasmid pST3606-1 and a 70.5-kb IncFII plasmid pST3606-2. The isolate carried resistance genes, including blaNDM-5, sul1, qacE, aadA2, and dfrA12 in pST3606-1, blaTEM-1B, aac(3)-lld, and blaCTX-M-261, a novel blaCTX-M-1 family member, in pST3606-2, and aac(6')-Iaa in chromosome. The blaCTX-M-261 was derived from blaCTX-M-55 by a single-nucleotide mutation 751G>A leading to amino acid substitution of Val for Met at position 251 (Val251Met), which conferred CTX-M increasing resistance to ceftazidime verified by antibiotics susceptibility testing of transconjugants carrying pST3606-2 and steady-state kinetic parameters of CTX-M-261. pST3606-1 is an IncI1-α incompatibility type that shares homology with plasmids of pC-F-164_A-OXA140, pE-T654-NDM-5, p_dm760b_NDM-5, and p_dmcr749c_NDM-5. The conjugation experiment demonstrated that pST3606-2 was successfully transferred to the Escherichia coli recipient C600 with four modules of OriTfinder.

CONCLUSION

Plasmid-mediated horizontal transfer plays an important role in blaNDM-5 and blaCTX-M-261 dissemination, which increases the threat to public health due to the resistance to most β-lactam antibiotics. This is the first report of blaCTX-M-261 and blaNDM-5 in S. 1,4,[5], 12: i: -. The work provides insights into the enzymatic function and demonstrates the ongoing evolution of CTX-M enzymes and confirms urgency to control resistance of S. 1,4,[5], 12: i: -.

Evaluation of the Lytic Activity of Various Phage Cocktails Against, ESBL-Producer, Non-Producer and Carbapenem-Resistant Escherichia coli Isolates

Bacteriophages have been proposed as an alternative therapy for the treatment of bacterial infections. This research aims to determine the lytic activity of bacteriophage-cocktails (BC) against carbapenem-resistant (CR-EC), ESBL-producer (EP-EC), and non-producer (NP-EC) E. coli isolates. Related resistance genes in 87 E. coli isolates were screened by PCR. The efficacies of BCs were determined by spot test and lytic zones were evaluated from fully-confluent to opaque. MOIs of the BCs were compared for fully-confluent and opaque lytic zones. BCs were also evaluated in terms of their biophysical characteristics including latency, burst size, pH and temperature stabilities. Among EP-EC, 96.9% of the isolates carry blaCTX-M, 25% of them blaSHV and 15.6% of them carry blaTEM. All CR-EC isolates carried blaOXA-48, but not blaKPC and blaNDM. CR-EC isolates were the least susceptible for the each of four BCs. MOIs for ENKO, SES and INTESTI-phage forming fully-confluent zone in E. coli isolates EC3 (NP-EC), EC8 (EP-EC) and EC27 (NP-EC), respectively were 10, 100 and 1, respectively. MOIs for ENKO, SES and INTESTI opaque zone in EC19 (EP-EC), EC10 (EP-EC), EC1(NP-EC), respectively were 0.01, 0.01, 0.1 PFU/CFU, respectively. The MOI for PYO-phage forming a semi-confluent zone in EC6 (NP-EC) isolate was 1 PFU/CFU. The phages were thermally stable and tolerant to a wide pH range. Comparison of MOIs according to lysis zone characteristics demonstrated that the activities of phages in phage cocktails vary depending on the characteristics of each bacterial host.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01074-9.

Genetic and Antimicrobial Resistance Profiles of Mammary Pathogenic E. coli (MPEC) Isolates from Bovine Clinical Mastitis

Mammary pathogenic E. coli (MPEC) is one of the main pathogens of environmental origin responsible for causing clinical mastitis worldwide. Even though E. coli are strongly associated with transient or persistent mastitis and the economic impacts of this disease, the virulence factors involved in the pathogenesis of MPEC remain unknown. Our aim was to characterize 110 MPEC isolates obtained from the milk of cows with clinical mastitis, regarding the virulence factor-encoding genes present, adherence patterns on HeLa cells, and antimicrobial resistance profile. The MPEC isolates were classified mainly in phylogroups A (50.9%) and B1 (38.2%). None of the isolates harbored genes used for diarrheagenic E. coli classification, but 26 (23.6%) and 4 (3.6%) isolates produced the aggregative or diffuse adherence pattern, respectively. Among the 22 genes investigated, encoding virulence factors associated with extraintestinal pathogenic E. coli pathogenesis, fimH (93.6%) was the most frequent, followed by traT (77.3%) and ompT (68.2%). Pulsed-field gel electrophoresis analysis revealed six pulse-types with isolates obtained over time, thus indicating persistent intramammary infections. The genes encoding beta-lactamases detected were as follows: bla_TEM (35/31.8%); bla_CTX-M-2/bla_CTX-M-8 (2/1.8%); bla_CTX-M-15 and bla_CMY-2 (1/0.9%); five isolates were classified as extended spectrum beta-lactamase (ESBL) producers. As far as we know, papA, shf, ireA, sat and bla_CTX-M-8 were detected for the first time in MPEC. In summary, the genetic profile of the MPEC studied was highly heterogeneous, making it impossible to establish a common genetic profile useful for molecular MPEC classification. Moreover, the detection of ESBL-producing isolates is a serious public health concern.

Comparative in vitro activities of omadacycline, eravacycline and tigecycline against non-ESBL-producing, ESBL-producing and carbapenem-resistant isolates of K. pneumoniae

Introduction. Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae and carbapenem-resistant Enterobacteriaceae are characterized by the World Health Organization as pathogens for which new antibiotics are urgently needed. Omadacycline and eravacycline are two novel antibacterials within the tetracycline class.

Gap Statement. There are limited data regarding the comparison of the activities of omadacycline, eravacycline and tigecycline against K. pneumoniae isolates with different antimicrobial susceptibility profiles.

Aim. Our objective was to compare the in vitro activities of omadacycline, eravacycline and tigecycline against a collection of K. pneumoniae isolates, including non-ESBL-producing, ESBL-producing and carbapenem-resistant strains.

Methodology. Ninety-four K. pneumoniae isolates, including 30 non-ESBL-producing, 30 ESBL-producing and 34 carbapenem-resistant (22 carrying bla OXA-48, 12 carrying bla NDM) strains were included in the study. ESBL and carbapenemase genes were detected by conventional PCR. Omadacycline, eravacycline and tigecycline MICs were determined by the gradient diffusion method and interpreted using US Food and Drug Administration (FDA)-defined breakpoints.

Results. Overall, the percentage of tigecycline-susceptible strains (97.9 %) was higher than the percentage of omadacyline-susceptible (75.5 %) and eravacycline-susceptible (72.3 %) strains. The omadacycline and eravacycline susceptibility rates were 83.3 % among non-ESBL-producing isolates and 66.7 % among ESBL-producing isolates. The most common ESBL gene detected was blaCTX -M (90 %), followed by bla TEM (50 %) and bla SHV (50 %). The omadacycline and eravacycline susceptibility rate among isolates carrying bla TEM was 33.3 %, whereas it was 100 % among isolates that do not carry bla TEM. The omadacycline and eravacycline susceptibility rates among carbapenem-resistant isolates were 76.5 and 67.6 %, respectively. The omadacycline susceptibility rates among bla OXA-48-positive and bla NDM-positive isolates were 77.3 and 75.0 %, respectively. The eravacycline susceptibility rates among bla OXA-48-positive and bla NDM-positive isolates were 68.2 and 66.7 %, respectively. One carbapenem-resistant isolate was intermediate and one ESBL-producing isolate was resistant to tigecycline.

Conclusion. Overall, tigecycline was the most active tetracycline against isolates. Omadacycline and eravacycline showed excellent activity against ESBL-producing K. pneumoniae isolates that do not carry bla TEM. Omadacycline showed reasonable activity against carbapenem-resistant K. pneumoniae isolates carrying bla OXA-48 or bla NDM.

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli survey in wild seabirds at a pristine atoll in the southern Atlantic Ocean, Brazil: First report of the O25b-ST131 clone harboring blaCTX-M-8

Antimicrobial resistance is among the most serious public health threats of the 21st century, with great impact in terms of One Health. Among antimicrobial resistant bacteria (ARB), extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) represent major challenges to human healthcare. Wild birds have been commonly used as environmental bioindicators of ESBL-EC. Remote locations represent a unique opportunity to evaluate the occurrence, dissemination and epidemiology of ARB in the environment. Herein we surveyed ESBL-EC in 204 cloacal swabs from six nonsynanthropic seabird species at the pristine Rocas Atoll, Brazil. We identified ESBL-EC isolates in 2.4% (5/204) of the tested seabirds, all in magnificent frigatebirds (Fregata magnificens). We isolated strains of O25b-ST131-fimH22 harboring gene bla_CTX-M-8 (3 clones), ST117 harboring gene bla_SHV-12, and a novel ST11350 (clonal complex 349) harboring genes bla_CTX-M-55 and fosA3. All the isolates presented Extraintestinal pathogenic E. coli (ExPEC) virulence profiles. We suggest that magnificent frigatebirds may act as "flying bridges", transporting ESBL-EC and ARGs from an anthropogenically-impacted archipelago geographically close to our pristine and remote study site. The characteristics of our isolates suggest zoonotic potential and, despite the apparent good health of all the evaluated birds, may represent a hypothetical potential threat to the avian population using the atoll. To our knowledge, this is the first description of: (1) the pandemic and public health relevant ST131-O25b harboring bla_CTX-M-8 worldwide; (2) ST131-fimH22 in wild birds; and (3); fosA3 in wildlife. Our findings expand the current epidemiological knowledge regarding host and geographical distribution of ESBL-EC and ARGs in wild birds, and emphasize the disseminating characteristics and adaptability of ST131 and ST117 strains within the human-animal-interface. Herein we discuss the involvement of nonsynanthropic wild birds in the epidemiology of antimicrobial resistance and their potential as sentinels of ESBL E. coli in insular environments.

Coexistence of virulence and β-lactamase genes in avian pathogenic Escherichia coli

Emergence of multidrug resistance in E. coli and advent of newer strains is becoming serious concern which requires keen observations. This study was designed to find the ciprofloxacin resistant E. coli isolates co-existed with multi-drug resistance along with β-lactamase production from poultry source, and finally the genome sequencing of these strains to explore genetic variations. Study constituted on isolation of n = 225 E. coli from broiler farms of central China which were further subjected to identification of resistance against ciprofloxacin followed by antibiogram of n = 26 antibiotics and identification of β-lactamase production. Whole genome resequencing was performed using Illumina HiSeq 4000 system. PCR results revealed predominant β-lactamase genes i.e.CTX-M, CTX-M-1, CTX-M3, TEM-1 and OXA. Furthermore, the MDR isolates were containing most of the tested virulence genes. The most prevalent virulence genes were pap-C, fim-C, fim-H, iuc-D, irp-2, tra-T, iro-N and iut-A. The single nucleotide polymorphisms (SNPs) loci mentioned in this data give valuable genetic markers to growing high-throughput techniques for fine-determination of genotyping of MDR and virulent isolates. Characterization of SNPs on functional basis shed new bits of knowledge on the evolution, disease transmission and pathogenesis of MDR E. coli isolates. In conclusion, these findings provide evidence that most of poultry E. coli are MDR, β-lactamase producers, and virulent which could be a zoonotic threat to the humans. The whole genome resequencing data provide higher resolution of resistance and virulence characteristics in E. coli which can further be used for the development of prevention and treatment strategies.

Occurrence of mcr-mediated colistin resistance in Salmonella clinical isolates in Thailand

Nontyphoidal Salmonella, an important zoonotic pathogen and a major cause of foodborne illnesses, could be a potential reservoir of plasmids harbouring mobile colistin resistance gene (mcr). This study reported, for the first time, a high rate of mcr-carrying Salmonella clinical isolates (3.3%, 24/724) in Thailand, associated with mcr-3 gene (3.0%, 22/724) in S. 4,[5],12:i:-(15.4%, 4/26), S. Typhimurium (8.8%, 5/57), and S. Choleraesuis (5.6%, 13/231). Remarkably, the increasing trends of colistin and extended-spectrum cephalosporin resistances have displayed a high agreement over the years, with a dramatic rise in the mcr-carrying Salmonella from 1.1% (6/563) during 2005–2007 to 11.2% (18/161) during 2014–2018 when CTX-M-55 became abundant. Clonal and plasmid analysis revealed that the self-transferable IncA/C and a novel hybrid IncA/C-FIIs MDR plasmids were the major vehicles to disseminate both mcr-3 and bla_CTX-M55 genes among diverse Salmonella strains, from as early as 2007. To our knowledge the occurrence of mcr-3 and the co-existence of it with bla_CTX-M-55 in S. Choleraesuis are reported here for the first time, leading to clinical concern over the treatment of the invasive salmonellosis. This study provides evidence of the potential reservoirs and vectors in the dissemination of the mcr and highlights the co-selection by colistin and/or cephalosporins.

Molecular characterization of antimicrobial resistance in Klebsiella pneumoniae isolated from Brazilian dairy herds

In this observational study, phenotypic and genotypic patterns of antimicrobial resistance (AMR) in Klebsiella pneumoniae isolated from intramammary infections, clinical mastitis, fresh feces, rectal swabs, animal hindlimbs, and bulk tank milk samples from Brazilian dairy herds were investigated. In addition, we identified specific genetic variants present among extended-spectrum β-lactamase (ESBL) producers. We obtained 169 isolates of K. pneumoniae from 2009 to 2011 on 24 Brazilian dairy farms located in 4 Brazilian states. The AMR profile of all isolates was determined using disk-diffusion assays. The antimicrobial panel included drugs commonly used as mastitis treatment in Brazilian dairy herds (gentamicin, cephalosporins, sulfamethoxazole-trimethoprim, tetracycline) as well as antimicrobials of critical importance for human health (meropenem, ceftazidime, fluoroquinolones). The K. pneumoniae isolates resistant to tetracycline, fluoroquinolones, sulfamethoxazole-trimethoprim, or chloramphenicol were screened for presence of drug-specific AMR genes [tet, qnr, aac(6')-Ib, floR, catA2, cm1A, dfr, sul] using PCR. In addition, we identified ESBL genes present among ESBL-producers by using whole genome sequencing. Genomes were assembled and annotated, and patterns of AMR genes were investigated. Resistance was commonly detected against tetracycline (22.5% of all isolates), streptomycin (20.7%), and sulfamethoxazole-trimethoprim (9.5%). Antimicrobial resistance rates were higher in K. pneumoniae isolated from intramammary infections in comparison with isolates from feces (19.2 and 0% of multidrug resistance in intramammary and fecal isolates, respectively). In contrast, no difference in AMR rates was observed when contrasting hind limbs and isolates from intramammary infections. The genes tetA, sul2, and floR were the most frequently observed AMR genes in K. pneumoniae resistant to tetracycline, sulfamethoxazole-trimethoprim, and chloramphenicol, respectively. The tetA gene was present exclusively in isolates from milk. The genes bla_CTX-M8 and bla_SHV-108 were present in 3 ESBL-producing K. pneumoniae, including an isolate from bulk tank milk. The 3 isolates were of sequence type 281 and had similar mobile genetic elements and virulence genes. Our study reinforced the epidemiological importance and dissemination of bla_CTX-M-8 pST114 plasmid in food-producing animals in Brazil.

Extended Spectrum β-Lactamase (ESBL) Producing Escherichia coli in Pigs and Pork Meat in the European Union

The aim of this article is to review the fast and worldwide distribution of ESBL enzymes and to describe the role of the pork production chain as a reservoir and transmission route of ESBL-producing Escherichia coli and ESBLs in the European Union (EU). The use of β-lactam antibiotics in swine production and the prevalence of ESBL producing E. coli in fattening pigs and pork meat across Europe is analyzed. Overall, an increasing trend in the prevalence of presumptive ESBL producing E. coli in fattening pigs in the EU has been observed in the last decade, although with major differences among countries, linked to different approaches in the use of antimicrobials in pork production within the EU. Moreover, the various dissemination pathways of these bacteria along the pork production chain are described, along with factors at farm and slaughterhouse level influencing the risk of introducing or spreading ESBL producing bacteria throughout the food chain.

High prevalence of atypical virulotype and genetically diverse background among Pseudomonas aeruginosa isolates from a referral hospital in the Brazilian Amazon

Pseudomonas aeruginosa is an opportunistic pathogen causing different types of infections, particularly in intensive care unit patients. Characteristics that favor its persistence artificial environments are related to its high adaptability, wide arsenal of virulence factors and resistance to several antimicrobial classes. Among the several virulence determinants, T3SS stands as the most important due to the clinical impact of exoS and exoU genes in patient’s outcome. The molecular characterization of P. aeruginosa isolates helps in the comprehension of transmission dynamics and enhance knowledge of virulence and resistance roles in infection process. In the present study, we investigated virulence and resistance properties and the genetic background of P. aeruginosa isolated from ICUs patients at a referral hospital in Brazilian Amazon. A total of 54 P. aeruginosa isolates were characterized by detecting 19 virulence-related genes, antimicrobial susceptibility testing, molecular detection of β-lactamase-encoding genes and genotyping by MLST and rep-PCR. Our findings showed high prevalence of virulence-related markers, where 53.7% of the isolates presented at least 17 genes among the 19 investigated (P = 0.01). The rare exoS⁺/exoU⁺ cytotoxic virulotype was detected in 55.6% of isolates. Antimicrobial susceptibility testing revealed percentages of antibiotic resistance above 50% to carbapenems, cephalosporins and fluoroquinolones associated to MDR/XDR isolates. Isolates harboring both bla_SPM-1 and bla_OXA genes were also detected. Genotyping methods demonstrated a wide genetic diversity of strains spread among the different intensive care units, circulation of international MDR/XDR high-risk clones (ST111, ST235, ST244 and ST277) and emergence of seven novel MLST lineages. Finally, our findings highlight the circulation of strains with high virulence potential and resistance to antimicrobials and may be useful on comprehension of pathogenicity process, treatment guidance and establishment of strategies to control the spread of epidemic P. aeruginosa strains.

Epidemic spread of IncI1/pST113 plasmid carrying the Extended-Spectrum Beta-Lactamase (ESBL) blaCTX-M-8 gene in Escherichia coli of Brazilian cattle

INTRODUCTION

The prevalence of Extended-Spectrum Beta-Lactamase (ESBL)-producing Enterobacteriaceae is increasing worldwide and the Agri-Food sector acts as a reservoir of clinically relevant ESBL genes. Our study aimed at detecting and characterizing ESBL-producing Enterobacteriaceae responsible for intestinal colonization of Brazilian bovines.

MATERIAL AND METHODS

ESBL-producing E. coli isolates were recovered from fecal samples of healthy cattle in Northwest Brazil. Antimicrobial susceptibility was determined by disk diffusion. Resistance and virulence genes were identified by PCR and amplicons were sequenced, clonality was assessed by PFGE and MLST, and plasmids were characterized by replicon typing, S1-PFGE and Southern blot hybridizations. Transferability of ESBL genes was assessed by conjugation assay.

RESULTS

A total of 40 ESBL-producing E. coli were characterized, which originated from 34/191 animals (17.8 %) and 15/22 farms (68.2 %). The bla_CTX-M-8 gene was the most frequent ESBL gene (62.5 %), followed by bla_SHV-2a (20.0 %), bla_CTX-M-2 (10.0 %), and bla_CTX-M-15 (7.5 %). The bla_CTX-M-8 gene was localized on the IncI1/pST113 plasmid in multiple E. coli sequence types across unrelated animals and farms.

DISCUSSION

We report the first characterization and a high prevalence of ESBL-producing E. coli in the beef cattle sector in Brazil, which is mainly supported by the spread of an epidemic IncI1/pST113/bla_CTX-M-8 plasmid. Since Brazil is one of the biggest beef meat exporters worldwide, the spread of this ESBL plasmid across other sectors, countries and continents should be considered with attention.

Genetics of Acquired Antibiotic Resistance Genes in Proteus spp

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

Carbapenem-Resistant Acinetobacter baumannii in Three Tertiary Care Hospitals in Mexico: Virulence Profiles, Innate Immune Response and Clonal Dissemination

Acinetobacter baumannii is one of the most important nosocomial pathogens distributed worldwide. Due to its multidrug-resistance and the propensity for the epidemic spread, the World Health Organization includes this bacterium as a priority health issue for development of new antibiotics. The aims of this study were to investigate the antimicrobial resistance profile, the clonal relatedness, the virulence profiles, the innate host immune response and the clonal dissemination of A. baumannii in Hospital Civil de Guadalajara (HCG), Hospital Regional General Ignacio Zaragoza (HRGIZ) and Pediatric ward of the Hospital General de México Eduardo Liceaga (HGM-P). A total of 252 A. baumannii clinical isolates were collected from patients with nosocomial infections in these hospitals between 2015 and 2016. These isolates showed a multidrug-resistant profile and most of them only susceptible to colistin. Furthermore, 83.3 and 36.9% of the isolates carried the bla_OXA–24 and bla_TEM–1 genes for resistance to carbapenems and β-lactam antibiotics, respectively. The clonal relatedness assessed by pulsed-field gel electrophoresis (PFGE) and by multi-locus sequence typing (MLST) demonstrated a genetic diversity. Remarkably, the ST136, ST208 and ST369 that belonged to the clonal complex CC92 and ST758 and ST1054 to the CC636 clonal complex were identified. The ST136 was a high-risk persistent clone involved in an outbreak at HCG and ST369 were related to the first carbapenem-resistant A. baumannii outbreak in HRGIZ. Up to 58% isolates were able to attach to A549 epithelial cells and 14.5% of them induced >50% of cytotoxicity. A549 cells infected with A. baumannii produced TNFα, IL-6 and IL-1β and the oxygen and nitrogen reactive species that contributes to the development of an inflammatory immune response. Up to 91.3% of clinical isolates were resistant to normal human serum activity. Finally, 98.5% of the clinical isolates were able to form biofilm over polystyrene tubes. In summary, these results demonstrate the increasingly dissemination of multidrug-resistant A. baumannii clones in three hospitals in Mexico carrying diverse bacterial virulence factors that could contribute to establishment of the innate immune response associated to the fatality risks in seriously ill patients.

Dissemination of Multidrug-Resistant Commensal Escherichia coli in Feedlot Lambs in Southeastern Brazil

Antimicrobial resistance (AR) is a public health issue since it limits the choices to treat infections by Escherichia coli in humans and animals. In Brazil, the ovine meat market has grown in recent years, but studies about AR in sheep are still scarce. Thus, this study aims to investigate the presence of AR in E. coli isolated from lambs during feedlot. To this end, feces from 112 lambs with 2 months of age, after weaning, were collected on the first day of the animals in the feedlot (day 0), and on the last day before slaughtering (day 42). Isolates were selected in MacConkey agar supplemented with 4 mg/L of ceftiofur and identified by biochemical methods. Isolates were submitted to an antimicrobial susceptibility test by disc-diffusion and PCR to investigate genes for phylogenetic group, virulence determinants and resistance to the several antimicrobial classes tested. The genetic localization of the bla genes detected was elucidated by S1-PFGE followed by Southern blot-hybridizations. The isolates were typed by XbaI-PFGE and MLST methods. Seventy-eight E. coli were isolated from 8/112 (7.1%) animals on day 0, and from 55/112 (49.1%) animals on day 42. Since only fimH was present in almost all E. coli (97.4%) as a virulence gene, and also 88.5% belonged to phylogroups B1 or A, we consider that isolates represent intestinal commensal bacteria. The dendrogram separated the 78 non-virulent isolates in seven clusters, two of which comprised 50 E. coli belonging to ST/CC 1727/446 or ST 3994 recovered on day 42 commonly harboring the genotype bla CMY -2-aac(3)-IIa -tetA-sul1-sul2-floR-cmlA. Special attention should be given to the presence of bla CTX-M-15, a worldwide gene spread, and bla CTX-M-14, a hitherto undetected gene in Enterobacteriaceae from food-producing animals in Brazil. Importantly, E. coli lineages and plasmids carrying bla genes detected here have already been reported as sources of infection in humans either from animals, food, or the environment, which raises public health concerns. Hence, two types of commensal E. coli carrying important AR genes clearly prevailed during feedlot, but lambs are also reservoirs of bacteria carrying important AR genes such as bla CTX-M-14 and bla CTX-M-15, mostly related to antimicrobial treatment failure.

Antimicrobial Resistance and Molecular Characterization of Extended-Spectrum β-Lactamases of Escherichia coli and Klebsiella spp. Isolates from Urinary Tract Infections in Southern Brazil

The objective of this study was to evaluate the frequency of different extended-spectrum β-lactamases (ESBL) as well as to associate these ESBL with antimicrobial (ATM) resistance in Escherichia coli and Klebsiella spp. isolates from outpatients and inpatients with urinary tract infections. The study included 435 consecutive nonduplicate clinical isolates, including 362 E. coli isolates, 62 Klebsiella pneumoniae isolates, and 11 K. oxytoca isolates. Isolates were obtained from patients who were treated in a University Hospital between August 2012 and July 2013. Three multiplex PCR were performed to identify the ESBL groups. A total of 48 (11%) ESBL-producing isolates were found. The risk for the ESBL presence was significantly higher in males (26.4%) than females (8%), from hospital-acquired infections (29.1%) than community-acquired infections (7.0%) and in Klebsiella spp. (27.4%) than in E. coli (7.7%). ESBL-producing isolates presented a significantly higher percentage of resistance in 21 of the 23 ATMs analyzed. The CTX-M-1 group was the most predominant ESBL identified. The bla_{CTX-M-1-group} gene was found in 56% of the total ESBL producers from community and in 42.4% from hospital origins; it was followed in frequency by the bla_{CTX-M-8/25-group}, also found in both environments. Klebsiella spp. presented the largest variety of β-lactamase enzyme combinations and a higher level of resistance to cefotaxime. These findings contribute to better knowledge of the epidemiology of ESBL enzymes and are alarming for the reduced therapeutic options available for the risk groups identified in the studied populations.

High prevalence of ceftriaxone resistance among invasive Salmonella enterica serotype Choleraesuis isolates in Thailand: The emergence and increase of CTX-M-55 in ciprofloxacin-resistant S. Choleraesuis isolates

S. Choleraesuis is a highly invasive zoonotic pathogen that causes a serious systemic infection in humans. The emergence and increase of resistance to ceftriaxone and ciprofloxacin among S. Choleraesuis has become a serious therapeutic problem. The present study demonstrated high frequency of antimicrobial resistance in Salmonella Choleraesuis among 414 nontyphoidal Salmonella isolates from bacteremic patients in Thailand. High rates of ceftriaxone (58.3%) and ciprofloxacin (19.6%) resistances were observed in S. Choleraesuis isolates. The dissemination of the self-transferable bla_CTX-M-14-carrying IncFII_s, IncFII, and IncI1 plasmids and bla_CMY-2-carrying IncA/C plasmid along with the clonal spread of bla_CMY-2-harbouring S. Choleraesuis isolates contributed to the high frequency of resistance to extended-spectrum cephalosporins (ESCs; third- and fourth-generation cephalosporins) during 2005-2007. We reported the first occurrence of ceftazidime-hydrolysing CTX-M-55 in S. Choleraesuis isolates which dramatically increased and became the most abundant CTX-M variant among ESC-resistant S. Choleraesuis isolates during 2012-2016. The spread of clone pulsotype B3 was due to the dissemination of IncA/C plasmids carrying both bla_CTX-M-55 and qnrS1 among ciprofloxacin-resistant S. Choleraesuis isolates harbouring D87G in GyrA. These isolates were apparently responsible for the high rates of co-resistance to ESCs and ciprofloxacin (51.3%) during 2012-2016. This study emphasizes the importance to have an action plan to control the dissemination of antimicrobial resistance in S. Choleraesuis since this poses a threat to global health due to travel and trade in animal food products.

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.

ESBL-producing Escherichia coli and Its Rapid Rise among Healthy People

Since around the 2000s, Escherichia coli (E. coli) resistant to both oxyimino-cephalosporins and fluoroquinolones has remarkably increased worldwide in clinical settings. The kind of E. coli is also identified in patients suffering from community-onset infectious diseases such as urinary tract infections. Moreover, recoveries of multi-drug resistant E. coli from the feces of healthy people have been increasingly documented in recent years, although the actual state remains uncertain. These E. coli isolates usually produce extended-spectrum β-lactamase (ESBL), as well as acquisition of amino acid substitutions in the quinolone-resistance determining regions (QRDRs) of GyrA and/or ParC, together with plasmid-mediated quinolone resistance determinants such as Qnr, AAC(6')-Ib-cr, and QepA. The actual state of ESBL-producing E. coli in hospitalized patients has been carefully investigated in many countries, while that in healthy people still remains uncertain, although high fecal carriage rates of ESBL producers in healthy people have been reported especially in Asian and South American countries. The issues regarding the ESBL producers have become very complicated and chaotic due to rapid increase of both ESBL variants and plasmids mediating ESBL genes, together with the emergence of various "epidemic strains" or "international clones" of E. coli and Klebsiella pneumoniae harboring transferable-plasmids carrying multiple antimicrobial resistance genes. Thus, the current state of ESBL producers outside hospital settings was overviewed together with the relation among those recovered from livestock, foods, pets, environments and wildlife from the viewpoint of molecular epidemiology. This mini review may contribute to better understanding about ESBL producers among people who are not familiar with the antimicrobial resistance (AMR) threatening rising globally.

Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken

Numerous studies have examined the prevalence of pathogenic Escherichia coli in poultry and poultry products; however, limited data are available regarding their resistance- and virulence-associated gene expression profiles. This study was designed to examine the resistance and virulence of poultry E. coli strains in vitro and in vivo via antibiotic susceptibility, biofilm formation and adhesion, and invasion and intracellular survivability assays in Caco-2 and Raw 264.7 cell lines as well as the determination of the median lethal dose in two-day old chickens. A clinical pathogenic multidrug-resistant isolate, E. coli 381, isolated from broilers, was found to be highly virulent in cell culture and 1000-fold more virulent in a chicken model than other strains; accordingly, the isolate was subsequently selected for transcriptome analysis. The comparative gene expression profile of MDR E. coli 381 and the reference human strain E. coli ATCC 25922 was completed with Illumina HiSeq. 2500 transcriptome analysis. Differential gene expression analysis indicates that there are multiple pathways involved in the resistance and virulence of this highly virulent strain. The results garnered from this study provide critical information about the highly virulent MDR E. coli strain of poultry origin and warrant further investigation due to its significant threat to public health.

Effects of feeding pasteurized waste milk to dairy calves on phenotypes and genotypes of antimicrobial resistance in fecal Escherichia coli isolates before and after weaning

The aim of this study was to evaluate the effects of feeding pasteurized waste milk (pWM) to calves on antimicrobial resistance of fecal Escherichia coli at both phenotypic and genotypic levels. Fifty-two Holstein female calves (3 ± 1.3 d of age) were fed 1 of the 2 different types of milk: milk replacer (MR) without antimicrobials or pWM with β-lactam residues until weaning at 49 d of age. Fecal swabs of all calves were obtained on d 0, 35, and 56 of the study and 3 E. coli isolates per sample were studied. Phenotypic resistance was tested by the disk diffusion method against a panel of 12 antimicrobials. A total of 13 resistance genes consisting of β-lactam, sulfonamide, tetracycline, and aminoglycoside families were examined by PCR. Feeding pWM to calves increased the presence of phenotypic resistance to ampicillin, cephalotin, ceftiofur, and florfenicol in fecal E. coli compared with MR-fed calves. However, the presence of resistance to sulfonamides, tetracyclines, and aminoglycosides was common in dairy calves independent of their milk-feeding source, suggesting other factors apart from the feeding source are involved in the emergence of antimicrobial resistance.

Designing of inhibitors against CTX-M-15 type β-lactamase: potential drug candidate against β-lactamases-producing multi-drug-resistant bacteria

CTX-M-15 are the most prevalent types of β-lactamases that hydrolyze almost all antibiotics of β-lactam group lead to multiple-antibiotic resistance in bacteria. Three β-lactam inhibitors are available for use in combination with different antibiotics of cephalosporine group against the CTX-M-15-producing strains. Therefore, strategies to identify novel anti β-lactamase agents with specific mechanisms of action are the need of an hour. In this study, we screened three novel non-β-lactam inhibitors against CTX-M-15 by multi-step virtual screening approach. The potential for virtually screened drugs was estimated through in vitro cell assays. Hence, we proposed a study to understand the binding mode of CTX-M-15 with inhibitors using bioinformatics and experimental approach. We calculated the dissociation constants (K_d), association constant (K_a), stoichiometry (n) and binding energies (ΔG) of compounds with the respective targets. Molecular dynamic simulation carried out for 25 ns, revealed that these complexes were found stable throughout the simulation with relative RMSD in acceptable range. Moreover, microbiological and kinetic studies further confirmed high efficacies of these inhibitors by reducing the minimum inhibitory concentration (MIC) and catalysis of antibiotics by β-lactamases in the presence of inhibitors. Therefore, we conclude that these potential inhibitors may be used as a lead molecule for future drug candidates against β-lactamases-producing bacteria.

Specific blaCTX-M-8/IncI1 Plasmid Transfer among Genetically Diverse Escherichia coli Isolates between Humans and Chickens

We investigated the genetic backbones of 14 bla_CTX-M-8-positive Escherichia coli isolates recovered from human stool samples and chicken meat. All isolates carried IncI1 plasmids with bla_CTX-M-8 (bla_CTX-M-8/IncI1), and most (9/14) belonged to a specific genetic lineage, namely, plasmid sequence type 113 (pST113). The genetic contexts of the nine bla_CTX-M-8/IncI1 pST113 plasmids were similar, regardless of the source. These results suggest the probable local transfer of bla_CTX-M-8/IncI1 between humans and chickens with genetically diverse E. coli.

Characterization of CTX-M enzymes, quinolone resistance determinants, and antimicrobial residues from hospital sewage, wastewater treatment plant, and river water

Multidrug-resistant (MDR) bacteria are widespread in hospitals and have been increasingly isolated from aquatic environments. The aim of the present study was to characterize extended-spectrum β-lactamase (ESBL) and quinolone-resistant Enterobacteriaceae from a hospital effluent, sanitary effluent, inflow sewage, aeration tank, and outflow sewage within a wastewater treatment plant (WWTP), as well as river water upstream and downstream (URW and DRW, respectively), of the point where the WWTP treated effluent was discharged. β-lactamase (bla) genes, plasmid-mediated quinolone resistance (PMQR), and quinolone resistance-determining regions (QRDRs) were assessed by amplification and sequencing in 55 ESBL-positive and/or quinolone-resistant isolates. Ciprofloxacin residue was evaluated by high performance liquid chromatography. ESBL-producing isolates were identified in both raw (n=29) and treated (n=26) water; they included Escherichia coli (32), Klebsiella pneumoniae (22) and Klebsiella oxytoca (1). Resistance to both cephalosporins and quinolone was observed in 34.4% of E. coli and 27.3% of K. pneumoniae. Resistance to carbapenems was found in 5.4% of K. pneumoniae and in K. oxytoca. Results indicate the presence of bla_CTX-M (51/55, 92.7%) and bla_SHV (8/55, 14.5%) ESBLs, and bla_GES (2/55, 3.6%) carbapenemase-encoding resistance determinants. Genes conferring quinolone resistance were detected at all sites, except in the inflow sewage and aeration tanks. Quinolone resistance was primarily attributed to amino acid substitutions in the QRDR of GyrA (47%) or to the presence of PMQR (aac-(6')-Ib-cr, oqxAB, qnrS, and/or qnrB; 52.9%) determinants. Ciprofloxacin residue was absent only from URW. Our results have shown strains carrying ESBL genes, PMQR determinants, and mutations in the gyrA QRDR genes mainly in hospital effluent, URW, and DRW samples. Antimicrobial use, and the inefficient removal of MDR bacteria and antibiotic residue during sewage treatment, may contribute to the emergence and spreading of resistance in the environment, making this a natural reservoir.

Prevalence of Extended-Spectrum β-Lactamases CTX-M-8 and CTX-M-2-Producing Salmonella Serotypes from Clinical and Nonhuman Isolates in Brazil

We characterized extended-spectrum β-lactamases (ESBL) enzymes among Salmonella strains isolated in Brazil from 2009 to 2014. Salmonella recovered from both clinical and nonhuman (food, poultry, and environment) sources were subjected to antimicrobial susceptibility testing. β-lactamases genes were detected by polymerase chain reaction/sequencing; plasmid profiles and transferability were assessed by S1-pulsed field gel electrophoresis (PFGE). Genetic diversity was evaluated by XbaI-PFGE. Out of 630 Salmonella strains screened, 46 displayed ESBL phenotype, distributed across 11 different serotypes. bla_CTX-M-8 and bla_CTX-M-2 genes were detected at frequencies of 47% and 41%, respectively. bla_SHV-5 and bla_SHV-2 were also detected but in lower frequencies (4%, 2%). bla_TEM-1 gene was detected in 22% of the strains. Most of the ESBL genes were transferable by conjugation, and the respective bla_ESBL gene was detected in the recipient strain, indicating the location of ESBL determinants on transferable plasmids. XbaI-PFGE revealed genomic diversity of Salmonella Typhimurium bearing bla_CTX-M-2, bla_CTX-M-8, bla_TEM-1, and bla_SHV-2 genes. Salmonella Muenchen (harboring bla_CTX-M-2) and Salmonella Corvallis (bla_CTX-M-8 and bla_SHV-5) showed clonal relatedness within respective serotypes. Our findings underscore the occurrence of diverse ESBL genes in several Salmonella serotypes, reinforcing the need for continuous surveillance of resistance genes circulating in human and nonhuman sources.

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.

Characterization of CTX-M-140, a Variant of CTX-M-14 Extended-Spectrum β-Lactamase with Decreased Cephalosporin Hydrolytic Activity, from Cephalosporin-Resistant Proteus mirabilis

CTX-M-140, a novel CTX-M-type extended-spectrum β-lactamase (ESBL), was identified in cephalosporin-resistant clinical isolates of Proteus mirabilis CTX-M-140 contained an alanine-to-threonine substitution at position 109 compared to its putative progenitor, CTX-M-14. When it was expressed in an Escherichia coli isogenic background, CTX-M-140 conferred 4- to 32-fold lower MICs of cephalosporins than those with CTX-M-14, indicating that the phenotype was attributable to this single substitution. For four mutants of CTX-M-14 that were constructed by site-directed mutagenesis (A109E, A109D, A109K, and A109R mutants), MICs of cephalosporins were similar to those for the E. coli host strain, which suggested that the alanine at position 109 was essential for cephalosporin hydrolysis. The kinetic properties of native CTX-M-14 and CTX-M-140 were consistent with the MICs for the E. coli clones. Compared with that of CTX-M-14, a lower hydrolytic activity against cephalosporins was observed for CTX-M-140. blaCTX-M-140 is located on the chromosome as determined by I-CeuI pulsed-field gel electrophoresis (I-CeuI-PFGE) and Southern hybridization. The genetic environment surrounding blaCTX-M-140 is identical to the sequence found in different plasmids with blaCTX-M-9-group genes among the Enterobacteriaceae Genome sequencing and analysis showed that P. mirabilis strains with blaCTX-M-140 have a genome size of ∼4 Mbp, with a GC content of 38.7% and 23 putative antibiotic resistance genes. Our results indicate that alanine at position 109 is critical for the hydrolytic activity of CTX-M-14 against oxyimino-cephalosporins.

Inhibitory activity of avibactam against selected β-lactamases expressed in an isogenic Escherichia coli strain

Avibactam restored the in-vitro antibacterial activity of ceftazidime, ceftaroline, and aztreonam against isogenic Escherichia coli expressing class A, class C, and class D β-lactamases. The enzymes included TEM and CTX-M extended spectrum β-lactamases, ACT, CMY and FOX AmpC-type enzymes, and carbapenemases including rarer KPC variants and OXA-139.

A Structure-Based Classification of Class A β-Lactamases, a Broadly Diverse Family of Enzymes

For medical biologists, sequencing has become a commonplace technique to support diagnosis. Rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. This is particularly true for data concerning class A β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. Many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. We analyzed several hundred amino acid sequences of class A β-lactamase enzymes for phylogenic relationships, the presence of specific residues, and cluster patterns. A clear distinction was first made between dd-peptidases and class A enzymes based on a small number of residues (S70, K73, P107, 130SDN132, G144, E166, 234K/R, 235T/S, and 236G [Ambler numbering]). Other residues clearly separated two main branches, which we named subclasses A1 and A2. Various clusters were identified on the major branch (subclass A1) on the basis of signature residues associated with catalytic properties (e.g., limited-spectrum β-lactamases, extended-spectrum β-lactamases, and carbapenemases). For subclass A2 enzymes (e.g., CfxA, CIA-1, CME-1, PER-1, and VEB-1), 43 conserved residues were characterized, and several significant insertions were detected. This diversity in the amino acid sequences of β-lactamases must be taken into account to ensure that new enzymes are accurately identified. However, with the exception of PER types, this diversity is poorly represented in existing X-ray crystallographic data.

Genetic background of novel sequence types of CTX-M-8- and CTX-M-15-producing Escherichia coli and Klebsiella pneumoniae from public wastewater treatment plants in São Paulo, Brazil

The release of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae to the environment is a public health issue worldwide. The aim of this study was to investigate the genetic background of genes encoding ESBLs in wastewater treatment plants (WWTPs) in São Paulo, southeastern Brazil. In 2009, during a local surveillance study, seven ESBL-producing Enterobacteriaceae strains were recovered from five WWTPs and screened for ESBL genes and mobile genetic elements. Multilocus sequence typing (MLST) was carried out, and wild plasmids were transformed into electrocompetent Escherichia coli. S1-PFGE technique was used to verify the presence of high molecular weight plasmids in wild-type strains and in bla ESBL-containing E. coli transformants. Strains harbored bla CTX-M-8, bla CTX-M-15, and/or bla SHV-28. Sequencing results showed that bla CTX-M-8 and bla CTX-M-15 genes were associated with IS26. MLST revealed new sequence types for E. coli (ST4401, ST4402, ST4403, and ST4445) and Klebsiella pneumoniae (ST1574), except for one K. pneumoniae from ST307 and Enterobacter cloacae from ST131. PCR and S1-PFGE results showed CTX-M-producing E. coli transformants carried heavy plasmids sizing 48.5-209 kb, which belonged to IncI1, IncF, and IncM1 incompatibility groups. This is the first report of CTX-M-8 and SHV-28 enzymes in environmental samples, and the present results demonstrate the plasmid-mediated spread of CTX-M-encoding genes through five WWTPs in São Paulo, Brazil, suggesting WWTPs are hotspots for the transfer of ESBL genes and confirming the urgent need to improve the management of sewage in order to minimize the dissemination of resistance genes to the environment.

Fast and Accurate Large-Scale Detection of β-Lactamase Genes Conferring Antibiotic Resistance

Fast detection of β-lactamase (bla) genes allows improved surveillance studies and infection control measures, which can minimize the spread of antibiotic resistance. Although several molecular diagnostic methods have been developed to detect limited bla gene types, these methods have significant limitations, such as their failure to detect almost all clinically available bla genes. We developed a fast and accurate molecular method to overcome these limitations using 62 primer pairs, which were designed through elaborate optimization processes. To verify the ability of this large-scale bla detection method (large-scaleblaFinder), assays were performed on previously reported bacterial control isolates/strains. To confirm the applicability of the large-scaleblaFinder, the assays were performed on unreported clinical isolates. With perfect specificity and sensitivity in 189 control isolates/strains and 403 clinical isolates, the large-scaleblaFinder detected almost all clinically available bla genes. Notably, the large-scaleblaFinder detected 24 additional unreported bla genes in the isolates/strains that were previously studied, suggesting that previous methods detecting only limited types of bla genes can miss unexpected bla genes existing in pathogenic bacteria, and our method has the ability to detect almost all bla genes existing in a clinical isolate. The ability of large-scaleblaFinder to detect bla genes on a large scale enables prompt application to the detection of almost all bla genes present in bacterial pathogens. The widespread use of the large-scaleblaFinder in the future will provide an important aid for monitoring the emergence and dissemination of bla genes and minimizing the spread of resistant bacteria.

IncI1/ST113 and IncI1/ST114 conjugative plasmids carrying blaCTX-M-8 in Escherichia coli isolated from poultry in Brazil

Extended-spectrum beta-lactamase-producing Escherichia coli isolated from poultry in Brazil showed blaCTX-M-8 gene. IS10 was found upstream of blaCTX-M-8, harbored on plasmids IncI1, ST113/ST114 subtypes. Genomic relationship revealed a heterogeneous E. coli population. The gene blaCTX-M-8 is established in South America in food-producing animals, which represent risk of dissemination for other countries.

Prevalence of the genes encoding extended-spectrum β-lactamases, inEscherichia coliresistant to β-lactam and non-β-lactam antibiotics

The prevalences of extended-spectrum beta-lactamases (ESBL) and their encoding bla genes, TEM, SHV and CTX_M, were investigated in isolates of Escherichia coli that were resistant to beta-lactam and/or non-beta-lactam antibiotics. Of the 250 E. coli isolates investigated, all of which came from patients in a major hospital in southern Lebanon, 61 (13.3%) were found to have ESBL, their production of beta-lactamase being confirmed by the ceftazidime and ceftazidime/clavulanic-acid disc methods. All 61 ESBL isolates were resistant to beta-lactams and sensitive to imipenem, piperacillin/tazobactam and cefoxitime. Only 40% were resistant to fluoroquinolones, 33% were resistant to aminoglycosides, and 18% were considered to have multi-drug resistance. The results of the PCR-based amplification of the bla gene in DNA samples from the 61 ESBL isolates indicated that 11 (18%) of the isolates carried both the TEM and SHV genes, 37 (61%) carried the TEM gene but not the SHV, and 13 (21%) had the SHV gene but not the TEM. None of the isolates carried the CTX_M gene. Of the 37 TEM-positive/SHV-negative isolates, 43% were resistant to fluoroquinolones and 37% to aminoglycosides. Increased resistance to non-beta-lactam antibiotics was observed in the isolates harbouring both the TEM and SHV genes, of which 54% were resistant to all of the tested antibiotics except imipenem, 36% were only resistant to fluoroquinolones, and 9.1% only resistant to aminoglycosides. The possibility that the concomitant presence of TEM- and SHV-type beta-lactamases is associated with resistance to non-beta-lactam antibiotics requires further research. The prevalences of ESBL and their encoding genes in Gram-negative bacteria collected from various regions in Lebanon will now be investigated.

Biochemical characterization of CTX-M-15 from Enterobacter cloacae and designing a novel non-β-lactam-β-lactamase inhibitor

The worldwide dissemination of CTX-M type β-lactamases is a threat to human health. Previously, we have reported the spread of bla_CTX-M-15 gene in different clinical strains of Enterobacteriaceae from the hospital settings of Aligarh in north India. In view of the varying resistance pattern against cephalosporins and other β-lactam antibiotics, we intended to understand the correlation between MICs and catalytic activity of CTX-M-15. In this study, steady-state kinetic parameters and MICs were determined on E. coli DH5α transformed with bla_CTX-M-15 gene that was cloned from Enterobacter cloacae (EC-15) strain of clinical background. The effect of conventional β-lactamase inhibitors (clavulanic acid, sulbactam and tazobactam) on CTX-M-15 was also studied. We have found that tazobactam is the best among these inhibitors against CTX-M-15. The inhibition characteristic of tazobactam is defined by its very low IC₅₀ value (6 nM), high affinity (K_i = 0.017 µM) and better acylation efficiency (k₊₂/K′ = 0.44 µM⁻¹s⁻¹). It forms an acyl-enzyme covalent complex, which is quite stable (k₊₃ = 0.0057 s⁻¹). Since increasing resistance has been reported against conventional β-lactam antibiotic-inhibitor combinations, we aspire to design a non-β-lactam core containing β-lactamase inhibitor. For this, we screened ZINC database and performed molecular docking to identify a potential non-β-lactam based inhibitor (ZINC03787097). The MICs of cephalosporin antibiotics in combination with this inhibitor gave promising results. Steady-state kinetics and molecular docking studies showed that ZINC03787097 is a reversible inhibitor which binds non-covalently to the active site of the enzyme through hydrogen bonds and hydrophobic interactions. Though, it’s IC₅₀ (180 nM) is much higher than tazobactam, it has good affinity for CTX-M-15 (K_i = 0.388 µM). This study concludes that ZINC03787097 compound can be used as seed molecule to design more efficient non-β-lactam containing β-lactamase inhibitor that could evade pre-existing bacterial resistance mechanisms.

Structural insights into the broadened substrate profile of the extended-spectrum β-lactamase OXY-1-1 fromKlebsiella oxytoca

Klebsiella oxytocais a pathogen that causes serious infections in hospital patients. It shows resistance to many clinically used β-lactam antibiotics by producing chromosomally encoded OXY-family β-lactamases. Here, the crystal structure of an OXY-family β-lactamase, OXY-1-1, determined at 1.93 Å resolution is reported. The structure shows that the OXY-1-1 β-lactamase has a typical class A β-lactamase fold and exhibits greater similarity to CTX-M-type β-lactamases than to TEM-family or SHV-family β-lactamases. It is also shown that the enzyme provides more space around the active cavity for theR1andR2substituents of β-lactam antibiotics. The half-positive/half-negative distribution of surface electrostatic potential in the substrate-binding pocket indicates the preferred properties of substrates or inhibitors of the enzyme. The results reported here provide a structural basis for the broadened substrate profile of the OXY-family β-lactamases.

Antibiotic resistance patterns of Acinetobacter calcoaceticus-A. baumannii complex species from Colombian hospitals

INTRODUCTION

Only automated phenotypic methods are currently used in Colombian hospitals for identifying isolates of the Acinetobacter calcoaceticus-A. baumannii complex (ACB). The phenotypical similarities in these species mean that they cannot be differentiated by manual or automated methods, thereby leading to their identification as A. baumannii, or ACB complex in clinical settings. Our objective was to identify to the species level 60 isolates, from four hospitals, evaluate their antibiotic susceptibility, and detect resistance-related genes.

METHODS

16S-23S rRNA internal transcribed spacer (ITS) region and rpoB gene partial sequences were amplified. Resistance genes for cephalosporin, carbapenem and aminoglycoside were detected by PCR. Possible mutations in the quinolone resistance-determining region (QRDR) were evaluated. The association of ISAba-1 with blaOXA and blaADC genes was determined by PCR. Amplification products of ITS region, rpoB gene and some resistance genes were sequenced and compared using the BLAST tool.

RESULTS

16S-23S rRNA ITS region and partial rpoB gene sequence analysis allowed 51isolates to be identified as A. baumannii, 8 as A. nosocomialis, and 1 isolate as A. pitti. A. baumannii isolates were highly resistant to all antibiotics tested, while the others were susceptible to ciprofloxacin and ampicillin/sulbactam. Quinolone resistance, found only in A. baumannii, was associated with mutations in the QRDR region of gyrA and parC genes.

CONCLUSION

This is the first investigation in Colombia that has identified ACB complex species using molecular methods, and determined differences in antibiotic resistance and resistance genes among the species. It is of the highest importance to identify isolates to the species level for future resistance and epidemiology studies in our region.

Diversity of genotypes in CTX-M-producing Klebsiella pneumoniae isolated in different hospitals in Brazil

OBJECTIVE

The present study was undertaken to characterize CTX-M ESBL-producing Klebsiella pneumoniae collected from hospitals in different cities of Brazil.

MATERIAL AND METHODS

Eighty-five K. pneumoniae strains isolated from hospitalized patients in six different hospitals of three cities of Brazil were analyzed. ESBL production was confirmed by the standard double-disk synergy test and the Etest®. The MIC50 and MIC90 for ESBL-producing isolates were determined by the Etest® method. The antimicrobial susceptibilities of bacterial isolates were determined using the agar diffusion method according to the CLSI. Screening for blaTEM, blaSHV, blaCTX-M genes and class 1 integron was performed by PCR amplification. To determine the genomic diversity of CTX-M-producers, isolates were analyzed by macrorestriction profile analysis following PFGE.

RESULTS AND DISCUSSION

Seventy-one K. pneumoniae isolates were ESBL-producing. PCR and sequencing experiments detected 38 CTX-M-producing K. pneumoniae belonged to groups CTX-M 1, CTX-M 2, CTX-M 8 and CTX-M 9. The association of different types ESBL (CTX-M, SHV and TEM) was frequent. All K. pneumoniae isolates carried class 1 integron. PFGE analysis revealed thirty-one clonal types among CTX-M-producing isolates. The data presented herein illustrate the diversity of genotypes of CTX-M producing K. pneumoniae among Brazilians hospitals.

Epidemiology and genetics of CTX-M extended-spectrum β-lactamases in Gram-negative bacteria

CTX-M enzymes, the plasmid-mediated cefotaximases, constitute a rapidly growing family of extended-spectrum β-lactamases (ESBLs) with significant clinical impact. CTX-Ms are found in at least 26 bacterial species, particularly in Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis. At least 109 members in CTX-M family are identified and can be divided into seven clusters based on their phylogeny. CTX-M-15 and CTX-M-14 are the most dominant variants. Chromosome-encoded intrinsic cefotaximases in Kluyvera spp. are proposed to be the progenitors of CTX-Ms, while ISEcp1, ISCR1 and plasmid are closely associated with their mobilization and dissemination.

Antibiotic resistance and plasmid transfer capacity in biofilm formed with a CTX-M-15-producing Klebsiella pneumoniae isolate

OBJECTIVES

To characterize a CTX-M-15-producing Klebsiella pneumoniae isolate that was identified during an outbreak involving 16 patients who had undergone endoscopic retrograde cholangiopancreatography between December 2008 and August 2009. The strain was also detected in one endoscope used for these examinations.

METHODS

Disc diffusion assays, MICs and isoelectric focusing were used to characterize the plasmidic CTX-M-15 β-lactamase. PCRs were used to check for the presence of genes associated with virulence or antibiotic resistance. Antibiotic tolerance tests and plasmid transfer were carried out in both planktonic and biofilm conditions.

RESULTS

The strain belonged to sequence type 14 and to the virulent capsular serotype K2, but produced little glucuronic acid. It contained a 62.5 kb conjugative plasmid carrying the bla(CTX-M-15), bla(OXA-1) and aac(6')-Ib-cr genes and harboured few virulence genes (uge, wabG, kfu and mrkD). The strain was highly resistant to cefotaxime (MIC 516 mg/L) and the presence of this antibiotic at sub-MIC concentrations enhanced biofilm formation. The isolate was susceptible to ofloxacin (MIC 2 mg/L), but the bactericidal effect of this antibiotic was greater in planktonic cultures and 6 h old biofilm than in 24 or 48 h old biofilms. The K. pneumoniae strain was notable for its ability to transfer its plasmid, especially in biofilm conditions, in which the rate of plasmid transfer was about 0.5/donor.

CONCLUSIONS

These findings demonstrate the ability of this strain to survive in a hospital environment and to transfer its extended-spectrum β-lactamase-encoding plasmid.

CTX-M Enzymes: Origin and Diffusion

CTX-M β-lactamases are considered a paradigm in the evolution of a resistance mechanism. Incorporation of different chromosomal bla_CTX-M related genes from different species of Kluyvera has derived in different CTX-M clusters. In silico analyses have shown that this event has occurred at least nine times; in CTX-M-1 cluster (3), CTX-M-2 and CTX-M-9 clusters (2 each), and CTX-M-8 and CTX-M-25 clusters (1 each). This has been mainly produced by the participation of genetic mobilization units such as insertion sequences (ISEcp1 or ISCR1) and the later incorporation in hierarchical structures associated with multifaceted genetic structures including complex class 1 integrons and transposons. The capture of these bla_CTX-M genes from the environment by highly mobilizable structures could have been a random event. Moreover, after incorporation within these structures, β-lactam selective force such as that exerted by cefotaxime and ceftazidime has fueled mutational events underscoring diversification of different clusters. Nevertheless, more variants of CTX-M enzymes, including those not inhibited by β-lactamase inhibitors such as clavulanic acid (IR-CTX-M variants), only obtained under in in vitro experiments, are still waiting to emerge in the clinical setting. Penetration and the later global spread of CTX-M producing organisms have been produced with the participation of the so-called “epidemic resistance plasmids” often carried in multi-drug resistant and virulent high-risk clones. All these facts but also the incorporation and co-selection of emerging resistance determinants within CTX-M producing bacteria, such as those encoding carbapenemases, depict the currently complex pandemic scenario of multi-drug resistant isolates.

Expression of OXA-type and SFO-1 β-lactamases induces changes in peptidoglycan composition and affects bacterial fitness

β-Lactamases and penicillin-binding proteins (PBPs) have evolved from a common ancestor. β-Lactamases are enzymes that degrade β-lactam antibiotics, whereas PBPs are involved in the synthesis and processing of peptidoglycan, which forms an elastic network in the bacterial cell wall. This study analyzed the interaction between β-lactamases and peptidoglycan and the impact on fitness and biofilm production. A representative set of all classes of β-lactamases was cloned in the expression vector pBGS18 under the control of the CTX-M promoter and expressed in Escherichia coli MG1655. The peptidoglycan composition of all clones was evaluated, and quantitative changes were found in E. coli strains expressing OXA-24, OXA-10-like, and SFO-1 (with its upstream regulator AmpR) β-lactamases; the level of cross-linked muropeptides decreased, and their average length increased. These changes were associated with a statistically significant fitness cost, which was demonstrated in both in vitro and in vivo experiments. The observed changes in peptidoglycan may be explained by the presence of residual DD-endopeptidase activity in these β-lactamases, which may result in hydrolysis of the peptide cross bridge. The biological cost associated with these changes provides important data regarding the interaction between β-lactamases and the metabolism of peptidoglycan and may provide an explanation for the epidemiology of these β-lactamases in Enterobacteriaceae.