Antimicrobial resistance among Enterobacteriaceae in South America: history, current dissemination status and associated socioeconomic factors

Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations

In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza and wild chimpanzees, identified similar bacterial richness and diversity surpassing those of westernized populations. While hominids share core bacterial communities, they also harbor distinct, population-specific bacterial taxa tailored to specific diets, ecology and lifestyles, differentiating non-indigenous and indigenous humans and chimpanzees. Even amongst shared bacterial communities, several core bacteria have co-diversified to fulfil unique dietary degradation functions within their host populations. These co-evolutionary trends extend to non-bacterial elements, such as mitochondrial DNA, antimicrobial resistance, and parasites. Our findings indicate that microbiome-host co-adaptations have led to both taxonomic and within taxa functional displacements to meet host physiological demands. The microbiome, in turn, transcends its taxonomic interchangeable role, reflecting the lifestyle, ecology and dietary history of its host.

Incidence of Extended Spectrum β-Lactamase Genes (ESBLs) among community and health care infection in Mansoura University Hospital, Egypt

BACKGROUND

Multidrug-resistant (MDR) Gram-negative bacteria pose a significant challenge due to their limited treatment options. The production of extended-spectrum β-lactamases (ESBLs) is an important mechanism of resistance. This study aimed to identify the incidence and characteristics of ESBL-encoding genes (blaCTX-M, blaTEM, blaSHV, and blaOXA) in MDR isolates.

MATERIALS AND METHODS

A cross-sectional study was conducted from September 2022 to May 2023. ESBL-producing isolates (n = 105) out of 412 were recovered from hospitalized and outpatient settings and analyzed. Standard microbiological methods were used for isolates identification, susceptibility testing, and phenotypic ESBL detection. Additionally, blaCTX-M, blaTEM, blaSHV, and blaOXA genes were identified using conventional PCR.

RESULTS

Molecular profiling of β-lactamase determinants was conducted via PCR targeting blaCTX-M, blaTEM, blaSHV, and blaOXA genes. Among phenotypically confirmed (100%) ESBL producers, 98% harbored one or more target genes, with blaCTX-M predominant (81%), followed by blaSHV (70.4%), blaTEM (62%), and blaOXA (30.4%). Carbapenem resistance was higher in ESBL-producing strains compared to non-ESBL strains. Extensively drug-resistant (XDR) isolates were the most common across hospital departments and outpatients.

DISCUSSION

This study highlights the significant prevalence of ESBL genes and multidrug resistance among Gram-negative bacteria. The dominance of blaCTX-M and the existence of multiple resistance genes raise concerns about limited treatment options. The findings emphasize the need for stricter antibiotic stewardship and infection control measures to curb the spread of MDR pathogens.

CONCLUSION

This study provides valuable insights into the alarming incidence of ESBL genes and MDR in Mansoura, Egypt. Continuous surveillance and implementation of effective control strategies are crucial to combat this growing public health threat.

In Silico Detection of Virulence Genes in Whole-Genome Sequences of Extra-Intestinal Pathogenic Escherichia coli (ExPEC) Documented in Countries of the Andean Community

E. coli pathotypes, which cause extra-intestinal infections, pose significant public health challenges, emphasizing the need for virulence gene surveillance to understand their dynamics. Key virulence genes have been identified in E. coli from Andean community countries, predominantly linked to human and animal sources. However, detailed data on virulence profiles from environmental and food sources remain limited. This study utilized an in silico approach to analyze 2402 whole-genome sequences from EnteroBase, known for associations with antimicrobial resistance genes. Of the isolates, 30% were classified as ExPEC, averaging 39 virulence genes per isolate, with adhesin-related genes being the most predominant. These findings were consistent across human, environmental, animal, and food samples. Human and animal isolates exhibited greater diversity in adhesin, secreted factors, and toxin genes compared to other sources, whereas food samples contained the fewest factors. ST449 isolates exhibited an average of 50 virulence genes per genome, with secreted factors and adhesins equally represented, while ST131, ST38, and ST10 carried around 40 genes, predominantly adhesins. Overall, the diversity and frequency of virulence genes exceeded prior reports in the region, highlighting the importance of monitoring these traits to identify emerging patterns in pathogenic E. coli strains frequently subjected to antibiotic exposure.

Pandemic one health clones of Escherichia coli and Klebsiella pneumoniae producing CTX-M-14, CTX-M-27, CTX-M-55 and CTX-M-65 ESβLs among companion animals in northern Ecuador

From a One Health perspective, dogs and cats have begun to be recognized as important reservoirs for clinically significant multidrug-resistant bacterial pathogens. In this study, we investigated the occurrence and genomic features of ESβL producing Enterobacterales isolated from dogs, in the province of Imbabura, Ecuador. We identified four isolates expressing ESβLs from healthy and diseased animals. In this regard, two Escherichia coli strains producing CTX-M-55-like or CTX-M-65 ESβLs belonged to the international ST10 and ST162, whereas two Klebsiella pneumoniae producing CTX-M-14 or CTX-M-27 belonged to ST35 and ST661. Phylogenomic analysis clustered (95-105 SNP differences) CTX-M-55/ST10 E. coli from companion animal with food and human E. coli strains of ST10 isolated in 2016, in Australia and Cambodia, respectively; whereas CTX-M-27-positive K. pneumoniae ST661 was clustered (201-216 SNP differences) with human strains identified in Italy, in 2013 and 2017, respectively. In summary, we report the presence and genomic data of global human-associated clones of CTX-M-producing E. coli and K. pneumoniae in dogs, in Ecuador. The implementation of a national epidemiological surveillance program is necessary to establish future strategies to control the dissemination of antibiotic-resistant priority pathogens using a One Health approach.

Unveiling the High Diversity of Clones and Antimicrobial Resistance Genes in Escherichia coli Originating from ST10 across Different Ecological Niches

In this pioneering in silico study in Peru, we aimed to analyze Escherichia coli (E. coli) genomes for antimicrobial resistance genes (ARGs) diversity and virulence and for its mobilome. For this purpose, 469 assemblies from human, domestic, and wild animal hosts were investigated. Of these genomes, three were E. coli strains (pv05, pv06, and sf25) isolated from chickens in our previous study, characterized for antimicrobial susceptibility profile, and sequenced in this study. Three other genomes were included in our repertoire for having rare cgMLSTs. The phenotypic analysis for antimicrobial resistance revealed that pv05, pv06, and sf25 strains presented multidrug resistance to antibiotics belonging to at least three classes. Our in silico analysis indicated that many Peruvian genomes included resistance genes, mainly to the aminoglycoside class, ESBL-producing E. coli, sulfonamides, and tetracyclines. In addition, through Multi-locus Sequence Typing, we found more than 180 different STs, with ST10 being the most prevalent among the genomes. Pan-genome mapping revealed that, with new lineages, the repertoire of accessory genes in E. coli increased, especially genes related to resistance and persistence, which may be carried by plasmids. The results also demonstrated several genes related to adhesion, virulence, and pathogenesis, especially genes belonging to the high pathogenicity island (HPI) from Yersinia pestis, with a prevalence of 42.2% among the genomes. The complexity of the genetic profiles of resistance and virulence in our study highlights the adaptability of the pathogen to different environments and hosts. Therefore, our in silico analysis through genome sequencing enables tracking the epidemiology of E. coli from Peru and the future development of strategies to mitigate its survival.

Hospital sewage in Brazil: a reservoir of multidrug-resistant carbapenemase-producing Enterobacteriaceae

The One Health concept recognizes that human health is clearly linked to the health of animals and the environment. Infections caused by bacteria resistant to carbapenem antibiotics have become a major challenge in hospitals due to limited therapeutic options and consequent increase in mortality. In this study, we investigated the presence of carbapenem-resistant Enterobacteriaceae in 84 effluent samples (42 from hospital and 42 from non-hospital) from Campo Grande, midwest Brazil. First, sewage samples were inoculated in a selective culture medium. Bacteria with reduced susceptibility to meropenem and ertapenem were then identified and their antimicrobial susceptibility was determined using the Vitek-2 system. The blaKPC genes were detected using PCR and further confirmed by sequencing. Carbapenem-resistant Enterobacteriaceae (CRE) were identified in both hospital (n=32) and non-hospital effluent (n=16), with the most common being Klebsiella pneumoniae and of the Enterobacter cloacae complex species. This is the first study to indicate the presence of the blaKPC-2 gene in carbapenem-resistant Enterobacteriaceae, classified as a critical priority by the WHO, in hospital sewage in this region. The dissemination of carbapenem antibiotic-resistant genes may be associated with clinical pathogens. Under favorable conditions and microbial loads, resistant bacteria and antimicrobial-resistance genes found in hospital sewage can disseminate into the environment, causing health problems. Therefore, sewage treatment regulations should be implemented to minimize the transfer of antimicrobial resistance from hospitals.

Spread and persistence of antimicrobial resistance genes in wastewater from human and animal sources in São Paulo, Brazil

The spread of antimicrobial resistance (AMR) through multiple reservoirs is a global concern. Wastewater is a critical AMR dissemination source, so this study aimed to assess the persistence of resistance genetic markers in wastewater using a culture-independent approach. Raw and treated wastewater samples (n = 121) from a wastewater treatment plant (WWTP), a human hospital, a veterinary hospital, and a pig farm were monthly collected and concentrated by filtration. DNA was extracted directly from filter membranes, and PCR was used in the qualitative search of 32 antimicrobial resistance genes (ARGs). Selected genes (blaCTX-M, blaKPC, qnrB, and mcr-1) were enumerated by quantitative real-time PCR (qPCR). Twenty-six ARGs were detected in the qualitative ARGs search, while quantitative data showed a low variation of the ARG's relative abundance (RA) throughout the months, especially at the human hospital and the WWTP. At the WWTP, despite significantly reducing the absolute number of gene copies/L after each treatment stage (p < 0.05), slight increases (p > 0.05) in the RAs of genes blaCTX-M, qnrB, and mcr-1 were observed in reused water (tertiary treatment) when compared with secondary effluent. Although the increase is not statistically significant, it is worth noting that there was some level of ARGs concentration after the disinfection process. No significant absolute or relative after-treatment quantification reductions were observed for any ARGs at the veterinary hospital or the pig farm. The spread of ARGs through sewage needs to be continuously addressed, because their release into natural environments may pose potential risks of exposure to resistant bacteria and impact local ecosystems.

ESBL-Producing Enterobacterales at the Human-Domestic Animal-Wildlife Interface: A One Health Approach to Antimicrobial Resistance in Piauí, Northeastern Brazil

The use, misuse, and overuse of antimicrobials is one of the main public health threats of the 21st century. We investigated the risk factor of the presence of extended-spectrum, cephalosporin-resistant Enterobacterales in feces of non-domestic and domestic birds and other domestic animals in Piauí State, northeast Brazil. We collected a total of 387 cloacal and rectal swab samples of free-living birds, domestic birds, and domestic mammals in five municipalities: Amarante, Água Branca, Lagoa Alegre, Parnaíba, and Teresina. A total of 59/387 (15.2%) of these samples harbored extended spectrum beta-lactamase (ESBL)-producing Enterobacterales. Using the MALDI-TOF technique, we identified fifty-seven samples as Escherichia coli and two samples as Klebsiella pneumoniae. Teresina and Parnaíba had the highest prevalence of animals with resistant bacteria (32.1% and 27.1%, respectively) and highest exposure risk factor (OR of 16.06 and 8.58, respectively, and p < 0.001 for all). Multidrug-resistant, ESBL-producing Enterobacterales were observed in 72.8% of the samples (43/59). For the free-living birds, the positive samples belonged to a great kiskadee (Pitangus sulphuratus) and a semipalmated sandpiper (Calidris pusilla) in migratory and resident species, respectively. For domestic animals, the swine samples showed the highest prevalence of antimicrobial resistance. The lack of access to veterinary care and information regarding antimicrobial therapy, along with the easy access to antimicrobials without medical prescription, favors the inadequate use of antimicrobials in Piauí.

Detecting Class 1 Integrons and Their Variable Regions in Escherichia coli Whole-Genome Sequences Reported from Andean Community Countries

Various genetic elements, including integrons, are known to contribute to the development of antimicrobial resistance. Class 1 integrons have been identified in E. coli isolates and are associated with multidrug resistance in countries of the Andean Community. However, detailed information on the gene cassettes located on the variable regions of integrons is lacking. Here, we investigated the presence and diversity of class 1 integrons, using an in silico approach, in 2533 whole-genome sequences obtained from EnteroBase. IntFinder v1.0 revealed that almost one-third of isolates contained these platforms. Integron-bearing isolates were associated with environmental, food, human, and animal origins reported from all countries under scrutiny. Moreover, they were identified in clones known for their pathogenicity or multidrug resistance. Integrons carried cassettes associated with aminoglycoside (aadA), trimethoprim (dfrA), cephalosporin (blaOXA; blaDHA), and fluoroquinolone (aac(6')-Ib-cr; qnrB) resistance. These platforms showed higher diversity and larger numbers than previously reported. Moreover, integrons carrying more than three cassettes in their variable regions were determined. Monitoring the prevalence and diversity of genetic elements is necessary for recognizing emergent patterns of resistance in pathogenic bacteria, especially in countries where various factors are recognized to favor the selection of resistant microorganisms.

Crisis averted: a world united against the menace of multiple drug-resistant superbugs -pioneering anti-AMR vaccines, RNA interference, nanomedicine, CRISPR-based antimicrobials, bacteriophage therapies, and clinical artificial intelligence strategies to safeguard global antimicrobial arsenal

The efficacy of antibiotics and other antimicrobial agents in combating bacterial infections faces a grave peril in the form of antimicrobial resistance (AMR), an exceedingly pressing global health issue. The emergence and dissemination of drug-resistant bacteria can be attributed to the rampant overuse and misuse of antibiotics, leading to dire consequences such as organ failure and sepsis. Beyond the realm of individual health, the pervasive specter of AMR casts its ominous shadow upon the economy and society at large, resulting in protracted hospital stays, elevated medical expenditures, and diminished productivity, with particularly dire consequences for vulnerable populations. It is abundantly clear that addressing this ominous threat necessitates a concerted international endeavor encompassing the optimization of antibiotic deployment, the pursuit of novel antimicrobial compounds and therapeutic strategies, the enhancement of surveillance and monitoring of resistant bacterial strains, and the assurance of universal access to efficacious treatments. In the ongoing struggle against this encroaching menace, phage-based therapies, strategically tailored to combat AMR, offer a formidable line of defense. Furthermore, an alluring pathway forward for the development of vaccines lies in the utilization of virus-like particles (VLPs), which have demonstrated their remarkable capacity to elicit a robust immune response against bacterial infections. VLP-based vaccinations, characterized by their absence of genetic material and non-infectious nature, present a markedly safer and more stable alternative to conventional immunization protocols. Encouragingly, preclinical investigations have yielded promising results in the development of VLP vaccines targeting pivotal bacteria implicated in the AMR crisis, including Salmonella, Escherichia coli, and Clostridium difficile. Notwithstanding the undeniable potential of VLP vaccines, formidable challenges persist, including the identification of suitable bacterial markers for vaccination and the formidable prospect of bacterial pathogens evolving mechanisms to thwart the immune response. Nonetheless, the prospect of VLP-based vaccines holds great promise in the relentless fight against AMR, underscoring the need for sustained research and development endeavors. In the quest to marshal more potent defenses against AMR and to pave the way for visionary innovations, cutting-edge techniques that incorporate RNA interference, nanomedicine, and the integration of artificial intelligence are currently under rigorous scrutiny.

The Prevalence of Metallo-Beta-Lactamese-(MβL)-Producing Pseudomonas aeruginosa Isolates in Brazil: A Systematic Review and Meta-Analysis

The purpose of the current study is to describe the prevalence of Pseudomonas aeruginosa (PA)-producing MβL among Brazilian isolates and the frequency of blaSPM-1 in MβL-PA-producing isolates. From January 2009 to August 2023, we carried out an investigation on this subject in the internet databases SciELO, PubMed, Science Direct, and LILACS. A total of 20 papers that met the eligibility requirements were chosen by comprehensive meta-analysis software v2.2 for data retrieval and analysis by one meta-analysis using a fixed-effects model for the two investigations. The prevalence of MβL-producing P. aeruginosa was 35.8% or 0.358 (95% CI = 0.324-0.393). The studies' differences were significantly different from one another (x2 = 243.15; p < 0.001; I2 = 92.18%), so they were divided into subgroups based on Brazilian regions. There was indication of asymmetry in the meta-analyses' publishing bias funnel plot; so, a meta-regression was conducted by the study's publication year. According to the findings of Begg's test, no discernible publishing bias was found. blaSPM-1 prevalence was estimated at 66.9% or 0.669 in MβL-PA isolates (95% CI = 0.593-0.738). The analysis of this one showed an average heterogeneity (x2 = 90.93; p < 0.001; I2 = 80.20%). According to the results of Begg's test and a funnel plot, no discernible publishing bias was found. The research showed that MβL-P. aeruginosa and SPM-1 isolates were relatively common among individuals in Brazil. P. aeruginosa and other opportunistic bacteria are spreading quickly and causing severe infections, so efforts are needed to pinpoint risk factors, reservoirs, transmission pathways, and the origin of infection.

Role of Brazilian bats in the epidemiological cycle of potentially zoonotic pathogens

Bats (Chiroptera) are flying mammals of great biodiversity and habits. These characteristics contribute for them being natural reservoirs and part of the epidemiological cycle of several potentially zoonotic pathogens, such as viruses, protozoa, fungi and bacteria. Brazil hosts approximately 15% of the world's bat diversity, with 181 distinct species, 68 genera and 9 families. About 60% of infectious diseases in humans are of zoonotic origin and, in the last decades, the detection of zoonotic pathogens in bats and their environment has been reported, such as Rabies virus (RABV) and Histoplasma capsulatum. Thus, the aim of this work was to review the reports of zoonotic pathogens associated with bats in Brazil in the past ten years. We reviewed the main pathogenic microorganisms described and the species of bats most frequently involved in the epidemiological cycles of these zoonotic agents. The obtained data show an upward trend in the detection of zoonotic pathogens in Brazilian bats, such as RABV, Bartonella sp., Histoplasma capsulatum and Leishmania spp., with emphasis on the bat species Artibeus lituratus, Carollia perspicillata, Desmodus rotundus and Molossus molossus. These findings highlight the importance of monitoring bat-associated microrganisms to early identify pathogens that may threaten bat populations, including potentially zoonotic microrganisms, emphasizing the importance of the One Health approach to prevent and mitigate the risks of the emergence of zoonotic diseases.

Enrofloxacin-induced transfer of multiple-antibiotic resistance genes and emergence of novel resistant bacteria in red swamp crayfish guts and pond sediments

Antibiotic resistance genes (ARGs) can be transferred from environmental microbes to human pathogens, thus leading to bacterial infection treatment failures. The aquaculture polluted by over-used antibiotics is considered as a notorious reservoir of ARGs. However, the origin, diachronic changes, and mobility of ARGs under antibiotic exposure in aquaculture systems remain elusive. Our findings showed that enrofloxacin application also increased the relative abundance of various ARGs in addition to quinolone-resistance genes and induced ARG dissemination in crayfish gut and sediment bacteria. Further investigation indicated that the transposase-mediated recombination was the major driver of horizontal gene transfer (HGT) of ARGs under antibiotic stress. Notably, enrofloxacin application also induced the generation of some metagenome-assembled genomes (MAGs) carrying multiple ARGs, which were identified as novel species. Additionally, Enterobacteriaceae constituted a mobile ARG pool in aquaculture. Therefore, aquaculture provides potential wide environmental pathways for generation and spread of antibiotic resistance. Our findings of ARG temporal variations and dissemination pattern in aquaculture with artificial use of antibiotics are critical to the management of antibiotic resistance, which is of great ecosystem and health implications.

Resistance determinants of emerging pathogens isolated from an intensive care unit as a parameter of population health conditions of the Legal Amazon microregion

Abstract Bacteria responsible for causing infections are common in hospital environments, water, soil, and food products. The infection risk is intensified by the absence of public sanitation, poor quality of life, and food scarcity. These external factors promote the dissemination of pathogens by direct contamination or biofilm formation. In this work, we identified bacterial isolates obtained from intensive care units in the southern region of Tocantins, Brazil. We compared matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) techniques and 16S ribosomal ribonucleic acid (rRNA) molecular analysis; we also performed phenotypic characterization. Fifty-six isolates characterized using morphotinctorial tests were classified as gram-positive (80.4%; n = 45) and gram-negative (19.6%; n = 11) and were resistant to several antibiotic classes; notably, we identified the blaOXA-23 resistance gene in the ILH10 isolate. Microbial identification using MALDI-TOF MS resulted in the identification of Sphingomonas paucimobilis and Bacillus circulans. 16S rRNA sequencing revealed four isolates belonging to the genera Bacillus and Acinetobacter. The similarity was superior to 99% for Acinetobacter schindleri in the Basic Local Alignment Search Tool (BLAST), grouped in the clade superior to 90%. Several strains isolated from intensive care units (ICU) were resistant to various antibiotic classes. These techniques allowed for the identification of several microorganisms of importance in public health, enabling improvements in human infection control and proving the quality of inputs, food, and water.

Rapid Detection of Carbapenemase and Extended-Spectrum β-Lactamase Producing Gram-Negative Bacteria Directly from Positive Blood Cultures Using a Novel Protocol

BACKGROUND

Early and adequate antibiotic treatment is the cornerstone of improving clinical outcomes in patients with bloodstream infections (BSI). Delays in appropriate antimicrobial therapy have catastrophic consequences for patients with BSI. Microbiological characterization of multi-drug resistant pathogens (MDRP) allows clinicians to provide appropriate treatments. Current microbiologic techniques may take up to 96 h to identify causative pathogens and their resistant patterns. Therefore, there is an important need to develop rapid diagnostic strategies for MDRP. We tested a modified protocol to detect carbapenemase and extended-spectrum β-lactamase (ESBL) producing Gram-negative bacteria (GNB) from positive blood cultures.

METHODS

This is a prospective cohort study of consecutive patients with bacteremia. We developed a modified protocol using the HB&L^® system to detect MDRP. The operational characteristics were analyzed for each test (HB&L-ESBL/AmpC^® and HB&L-Carbapenemase^® kits). The kappa coefficient, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), likelihood ratios (LR) with 95% confidence intervals (CI), and reduction in identification time of this novel method were calculated.

RESULTS

Ninety-six patients with BSI were included in the study. A total of 161 positive blood cultures were analyzed. Escherichia coli (50%, 81/161) was the most frequently identified pathogen, followed by Klebsiella pneumoniae (15%, 24/161) and Pseudomonas aeruginosa (8%, 13/161). Thirty-three percent of isolations had usual resistance patterns. However, 34/161 (21%) of identified pathogens were producers of carbapenemases and 21/161 (13%) of extended-spectrum β-lactamases. Concordance between our HB&L^® modified protocol and the traditional method was 99% (159/161). Finally, identification times were significantly shorter using our HB&L^®-modified protocol than traditional methods: median (IQR) 19 h (18, 22) vs. 61 h (60, 64), p < 0.001.

CONCLUSIONS

Here, we provide novel evidence that using our HB&L^®-modified protocol is an effective strategy to reduce the time to detect MDRP producers of carbapenemases or extended-spectrum β-lactamases, with an excellent concordance rate when compared to the gold standard. Further studies are needed to confirm these findings and to determine whether this method may improve clinical outcomes.

A Survey on the Rationale Usage of Antimicrobial Agents in Small Animal Clinics and Farms in Trinidad and Jamaica

The extensive and indiscriminate use of antibiotics is known to contribute to antimicrobial resistance. Unfortunately, there are no public records of antimicrobial use (frequency or dosage) administered to animals in two major CARICOM (Caribbean Community) countries: Trinidad and Tobago, and Jamaica. Surveillance would promote amendments and discussion on a Caribbean antimicrobial-use protocol. In this study, an online survey was conducted using cross-sectional qualitative interviews via email, targeting veterinary clinicians working in clinics and farms in Trinidad and Jamaica, to identify how antimicrobials are used in the two countries. Out of the thirty-two (32) clinicians interviewed in Trinidad, 22 (68.75%) were small animal practitioners, and 10 (45.45%) were mixed practitioners. While in Jamaica, a total of Twenty six (26) clinicians responded, of which 17 of them (65.38%) were small animal practitioners and nine (34.62%) were mixed practitioners. A total of 95.2% of clinics and farms in Jamaica and 87.1% in Trinidad did not use standard antimicrobial protocols, which could be due to the limited availability of resources. The broad-spectrum antibiotic, amoxicillin, and amoxicillin/clavulanic acid were the most commonly used drugs in small animal practices in both countries (71.9% and 53.8% in dogs), (78.1% and 65.9% in cats); amoxicillin is also used frequently in mixed animal practice in Jamaica (44.4% in goats, 33.3% in cattle and 22.2% in sheep and pigs), while procaine penicillin and streptomycin was the most frequently used in mixed practice in Trinidad (60% in cattle and goats, 50% in sheep), which could explain the potentially increased risk of antimicrobial resistance.

Whole-Genome Characterisation of ESBL-Producing E. coli Isolated from Drinking Water and Dog Faeces from Rural Andean Households in Peru

E. coli that produce extended-spectrum β-lactamases (ESBLs) are major multidrug-resistant bacteria. In Peru, only a few reports have characterised the whole genome of ESBL enterobacteria. We aimed to confirm the identity and antimicrobial resistance (AMR) profile of two ESBL isolates from dog faeces and drinking water of rural Andean households and determine serotype, phylogroup, sequence type (ST)/clonal complex (CC), pathogenicity, virulence genes, ESBL genes, and their plasmids. To confirm the identity and AMR profiles, we used the VITEK®2 system. Whole-genome sequencing (WGS) and bioinformatics analysis were performed subsequently. Both isolates were identified as E. coli, with serotypes -:H46 and O9:H10, phylogroups E and A, and ST/CC 5259/- and 227/10, respectively. The isolates were ESBL-producing, carbapenem-resistant, and not harbouring carbapenemase-encoding genes. Isolate 1143 ST5259 harboured the astA gene, encoding the EAST1 heat-stable toxin. Both genomes carried ESBL genes (blaEC-15, blaCTX-M-8, and blaCTX-M-55). Nine plasmids were detected, namely IncR, IncFIC(FII), IncI, IncFIB(AP001918), Col(pHAD28), IncFII, IncFII(pHN7A8), IncI1, and IncFIB(AP001918). Finding these potentially pathogenic bacteria is worrisome given their sources and highlights the importance of One-Health research efforts in remote Andean communities.

TEM,CTX-M,SHV Genes in ESBL-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Clinical Samples in a County Clinical Emergency Hospital Romania-Predominance of CTX-M-15

Background: CTX-M betalactamases have shown a rapid spread in the recent years among Enterobacteriaceae and have become the most prevalent Extended Spectrum Beta-Lactamases (ESBLs) in many parts of the world. The introduction and dissemination of antibiotic-resistant genes limits options for treatment, increases mortality and morbidity in patients, and leads to longer hospitalization and expensive costs. We aimed to identify the beta-lactamases circulating encoded by the genes bla_CTX-M-15, bla_SHV-1 and bla_TEM-1 in Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) strains. Furthermore, we established the associated resistance phenotypes among patients hospitalized in the Intensive Care Unit (ICU) from County Clinical Emergency Hospital of Craiova, Romania. Methods: A total of 46 non-duplicated bacterial strains (14 strains of E. coli and 32 strains of K. pneumoniae), which were resistant to ceftazidime (CAZ) and cefotaxime (CTX) by Kirby–Bauer disk diffusion method, were identified using the automated VITEK2 system. Detection of ESBL-encoding genes and other resistance genes was carried out by PCR. Results. E. coli strains were resistant to 3rd generation cephalosporins and moderately resistant to quinolones, whereas K. pneumoniae strains were resistant to penicillins, cephalosporins, and sulfamides, and moderately resistant to quinolones and carbapenems. Most E. coli strains harbored bla_CTX-M-15 gene (13/14 strains), a single strain had the bla_SHV-1 gene, but 11 strains harbored bla_TEM-1 gene. The mcr-1 gene was not detected. We detected tet(A) gene in six strains and tet(B) in one strain. In K. pneumoniae strains we detected bla_CTX-M-15 in 23 strains, bla_SHV-₁ in all strains and bla_TEM-1 in 14 strains. The colistin resistance gene mcr-1 was not detected. The tetracycline gene tet(A) was detected in 11 strains, but the gene tet(B) was not detected in any strains. Conclusions. The development in antibiotic resistance highlights the importance of establishing policies to reduce antibiotic use and improving the national resistance surveillance system in order to create local antibiotic therapy guidelines.

Anthropogenic Activities and the Problem of Antibiotic Resistance in Latin America: A Water Issue

Antibiotics revolutionized modern medicine and have been an excellent tool to fight infections. However, their overuse and misuse in different human activities such as health care, food production and agriculture has resulted in a global antimicrobial resistance crisis. Some regions such as Latin America present a more complex scenario because of the lack of resources, systematic studies and legislation to control the use of antimicrobials, thus increasing the spread of antibiotic resistance. This review aims to summarize the state of environmental antibiotic resistance in Latin America, focusing on water resources. Three databases were searched to identify publications on antimicrobial resistance and anthropogenic activities in relation to natural and artificial water ecosystems. We found that antibiotic resistant bacteria, mainly against beta lactam antibiotics, have been reported in several Latin American countries, and that resistant bacteria as well as resistant genes can be isolated from a wide variety of aquatic environments, including drinking, surface, irrigation, sea and wastewater. It is urgent to establish policies and regulations for antibiotic use to prevent the increase of multi-drug resistant microorganisms in the environment.

Biofilm Formation and Phenotypic Detection of ESBL, MBL, KPC and AmpC Enzymes and Their Coexistence in Klebsiella spp. Isolated at the National Reference Laboratory, Kathmandu, Nepal

Klebsiella spp. are associated with several nosocomial and opportunistic infections. Increasing antimicrobial resistance of Klebsiella species is aggravated by a number of intrinsic and extrinsic factors. The main aim of this study is to determine antimicrobial resistance due to production of β-lactamase enzymes, extended spectrum beta-lactamase (ESBL), metallo-beta-lactamase (MBL) and AmpC and Klebsiella pneumoniae carbapenemase (KPC) and biofilm formation in Klebsiella isolates. A total of 2197 non-duplicate specimens of urine, sputum and pus were obtained from the National Public Health Laboratory (NPHL), Kathmandu, Nepal, between February and August 2019. Klebsiella species were isolated, identified and screened for antimicrobial susceptibility testing with the disk diffusion method. Phenotypic detection of ESBL, MBL, KPC and AmpC production was observed and biofilm production was detected by the microtiter plate method. Out of a total of 2197 clinical specimens, bacterial growth was detected in 8% (175/2197) of the specimens. Of the total isolates, 86.3% (151/175) were Gram-negative bacteria and 37.7% (57/151) were Klebsiella spp. Of the total Klebsiella spp., 56% (32/57) were multi drug resistant (MDR), 16% (9/57) were ESBL, 26% (15/57) were MBL, 4% (2/57) were KPC (class A carbapenemase), 16% (9/57) were AmpC producers and 95% (54/57) were biofilm producers. Gentamicin was the most effective antibiotic, followed by cotrimoxazole, as 68% (39/57) and 47% (27/57) of the Klebsiella isolates were susceptible towards these drugs, respectively. The study results show evidence of β-lactamase production, high prevalence of MDR and biofilm producing Klebsiella species. Integrating the test parameters for phenotypic confirmation of ESBL, MBL, AmpC β lactamase and KPC in routine diagnostic procedures can help in the early detection and management of these resistant strains.

Acquisition of antimicrobial resistance determinants in Enterobacterales by international travelers from a large urban setting in Brazil

BACKGROUND

Antimicrobial resistance is increased by international mobility. We present data about intestinal colonization of travelers departing from a middle-income country.

METHODS

Travelers were recruited from 2015 to 2019, collected an anal stool specimen and answered a questionnaire before and after travel. Enterobacterales isolates were investigated for antimicrobial resistance; extended-spectrum beta-lactamase (ESBL) and carbapenemase production; plasmid-encoded cephalosporinases (pAmpC), plasmid-mediated quinolone resistance (PMQR) and mcr genes by PCR and sequencing; and association with travel related variables.

RESULTS

Among 210 travelers, 26 (12%) carried multidrug-resistant Enterobacterales (MDR-E) and 18 (9%) ESBL-producing Enterobacterales (ESBL-E) before travel, with an increased prevalence from 1% to 11% over the study years. Acquisition of MDR-E and ESBL-E occurred in 59 (32%) and 43 (22%) travelers, respectively, mostly bla_CTX-M-15 carrying Escherichia coli. One traveler acquired one isolate carrying bla_OXA-181 gene, and two others, isolates carrying mcr-1. PMQR were detected in 14 isolates of returning travelers. The risk of MDR-E acquisition was higher in Southeast Asia and the Indian subcontinent, and after using antimicrobial agents.

CONCLUSION

We describe an increasing pre-travel prevalence of ESBL-E colonization in subjects departing from this middle-income country over time. Travel to known risk areas and use of antimicrobial agents during travel were associated with acquisition of MDR-E. Travel advice is critical to mitigating this risk, as colonization by MDR-E may raise the chances of antimicrobial-resistant infections.

Antimicrobial-resistant enterobacteria in surface waters with fecal contamination from urban and rural communities

INTRODUCTION:

Inadequate wastewater treatment and fecal contamination have a strong environmental impact on antimicrobial resistance (AMR). This study evaluated the profile of AMR enterobacteria and fecal contamination from four surface waters: Jiquiriça-Brejões River and Cabrito, Tororó, and Abaeté Lagoons.

METHODS:

We analyzed AMR β-lactamase genes using the polymerase chain reaction method and fecal contamination using Coliscan^®.

RESULTS:

We found high levels of fecal contamination, β-lactamase producers, and AMR genes (bla_OXA-48, bla_SPM, and bla_VIM) in all waterbodies.

CONCLUSIONS:

Poor sanitation evidenced by fecal contamination and human activities around these surface waters contributed to the distribution and increase in AMR enterobacteria.

Microbial source tracking and antimicrobial resistance in one river system of a rural community in Bahia, Brazil

Use of antibiotics inevitably leads to antimicrobial resistance. Selection for resistance occurs primarily within the gut of humans and animals as well as in the environment through natural resistance and residual antibiotics in streams and soil. We evaluated antimicrobial resistance in Gram negative bacteria from a river system in a rural community in Bahia, Brazil. Water was collected from the Jiquiriçá and Brejões rivers and the piped water supply. Additionally, stools were collected from a random sample of residents, cows, pigs and horses near the river. The samples were screened for bacteria resistant to ciprofloxacin, cefotaxime, and meropenem and identified biochemically at the genus and species levels. Microbial source tracking demonstrated that ruminant and human fecal contamination increased as the rivers neared the village center and decreased after the last residence. Antibiotic bacteria were identified from all samples (n = 32). No bacteria were resistant to carbapenems, but the majority of the enterobacteria were resistant to ciprofloxacin, even though this class of antibiotics is not commonly used in food animals in this region. Considering these facts, together with the pattern of human fecal contamination, a human source was considered most likely for these resistant isolates.

Caretaker knowledge, attitudes, and practices (KAP) and carriage of extended-spectrum beta-lactamase-producing E. coli (ESBL-EC) in children in Quito, Ecuador

Background

The rapid spread of extended-spectrum beta-lactamase-producing E. coli (ESBL-EC) is an urgent global health threat. We examined child caretaker knowledge, attitudes, and practices (KAP) towards proper antimicrobial agent use and whether certain KAP were associated with ESBL-EC colonization of their children.

Methods

Child caretakers living in semi-rural neighborhoods in peri-urban Quito, Ecuador were visited and surveyed about their KAP towards antibiotics. Fecal samples from one child (less than 5 years of age) per household were collected at two time points between July 2018 and May 2019 and screened for ESBL-EC. A repeated measures analysis with logistic regression was used to assess the relationship between KAP levels and child colonization with ESBL-EC.

Results

We analyzed 740 stool samples from 444 children living in households representing a range of environmental conditions. Of 374 children who provided fecal samples at the first household visit, 44 children were colonized with ESBL-EC (11.8%) and 161 were colonized with multidrug-resistant E. coli (43%). The prevalences of ESBL-EC and multidrug-resistant E. coli were similar at the second visit (11.2% and 41.3%, respectively; N = 366). Only 8% of caretakers knew that antibiotics killed bacteria but not viruses, and over a third reported that they “always” give their children antibiotics when the child’s throat hurts (35%). Few associations were observed between KAP variables and ESBL-EC carriage among children. The odds of ESBL-EC carriage were 2.17 times greater (95% CI: 1.18–3.99) among children whose caregivers incorrectly stated that antibiotics do not kill bacteria compared to children whose caregivers correctly stated that antibiotics kill bacteria. Children from households where the caretaker answered the question “When your child’s throat hurts, do you give them antibiotics?” with “sometimes” had lower odds of ESBL-EC carriage than those with a caretaker response of “never” (OR 0.48, 95% CI 0.27–0.87).

Conclusion

Caregivers in our study population generally demonstrated low knowledge regarding appropriate use of antibiotics. Our findings suggest that misinformation about the types of infections (i.e. bacterial or viral) antibiotics should be used for may be associated with elevated odds of carriage of ESBL-EC. Understanding that using antibiotics is appropriate to treat infections some of the time may reduce the odds of ESBL-EC carriage. Overall, however, KAP measures of appropriate use of antibiotics were not strongly associated with ESBL-EC carriage. Other individual- and community-level environmental factors may overshadow the effect of KAP on ESBL-EC colonization. Intervention studies are needed to assess the true effect of improving KAP on laboratory-confirmed carriage of antimicrobial resistant bacteria, and should consider community-level studies for more effective management.

Prevalence and molecular characterisation of carbapenemase-producing Enterobacterales in an outbreak-free setting in a single hospital in Uruguay

OBJECTIVES

This study aimed to characterise all carbapenemase-producing enterobacteria (CPE) isolates obtained from an outbreak-free setting in Uruguay.

METHODS

We studied 12 CPE isolated from Hospital de Clínicas between 2012-2016. Bacterial identification and antibiotic susceptibility testing were performed using VITEK®2 and Sensititre or agar dilution, respectively. Antimicrobial resistance genes and mobile genetic elements were identified by PCR and sequencing. Multilocus sequence typing was performed for Klebsiella pneumoniae. Plasmid conjugation was assessed, plasmid size was estimated by S1-PFGE and plasmid incompatibility groups were sought by PCR.

RESULTS

Among 8364 enterobacteria, 12 CPE were isolated from urine, blood culture, wound, peritoneal fluid and punch samples. NDM-1 was the most prevalent carbapenemase, followed by VIM-2 and KPC-2. All isolates were resistant to gentamicin, cefotaxime, ceftazidime, trimethoprim/sulfamethoxazole, ciprofloxacin and imipenem and were susceptible to fosfomycin. We characterised six class 1 integrons: dfrA12-orfF-aadA2; aacA4-bla_OXA-2-orfD; aadB-aadA2; dfrA1; aadB-bla_OXA-10-aadA1; and bla_VIM-2-dfrA7. An association between various aminoglycoside, β-lactam and fluoroquinolone resistance genes were observed, some of them located in transferable plasmids belonging to incompatibility groups IncC, IncHI1 and IncM1. We described a new composite transposon (assigned Tn6935) including bla_NDM-1 flanked by two directly-oriented copies of a Tn3-like element ISKox2-like family transposase. The sequence types of K. pneumoniae isolates were ST11, ST14 and ST661.

CONCLUSIONS

The presence of CPE is sporadic and could be due to measures taken by the Public Health Committee. Nevertheless, the coexistence of several resistance mechanisms and their presence in conjugative plasmids and high-risk clones is worrisome.

Community-Acquired Antimicrobial Resistant Enterobacteriaceae in Central America: A One Health Systematic Review

Community-acquired antimicrobial resistant Enterobacteriaceae (CA-ARE) are an increasingly important issue around the world. Characterizing the distribution of regionally specific patterns of resistance is important to contextualize and develop locally relevant interventions. This systematic review adopts a One Health framework considering the health of humans, animals, and the environment to describe CA-ARE in Central America. Twenty studies were identified that focused on antimicrobial resistance (AMR) in Enterobacteriaceae. Studies on CA-ARE in Central America characterized resistance from diverse sources, including humans (n = 12), animals (n = 4), the environment (n = 2), and combinations of these categories (n = 2). A limited number of studies assessed prevalence of clinically important AMR, including carbapenem resistance (n = 3), third generation cephalosporin resistance (n = 7), colistin resistance (n = 2), extended spectrum beta-lactamase (ESBL) production (n = 4), or multidrug resistance (n = 4). This review highlights significant gaps in our current understanding of CA-ARE in Central America, most notably a general dearth of research, which requires increased investment and research on CA-ARE as well as AMR more broadly.

Socioeconomic factors associated with antimicrobial resistance of Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli in Chilean hospitals (2008-2017)

Objective.

To identify socioeconomic factors associated with antimicrobial resistance of Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli in Chilean hospitals (2008–2017).

Methods.

We reviewed the scientific literature on socioeconomic factors associated with the emergence and dissemination of antimicrobial resistance. Using multivariate regression, we tested findings from the literature drawing from a longitudinal dataset on antimicrobial resistance from 41 major private and public hospitals and a nationally representative household survey in Chile (2008–2017). We estimated resistance rates for three priority antibiotic–bacterium pairs, as defined by the Organisation for Economic Co-operation and Development; i.e., imipenem and meropenem resistant P. aeruginosa, cloxacillin resistant S. aureus, and cefotaxime and ciprofloxacin resistant E. coli.

Results.

Evidence from the literature review suggests poverty and material deprivation are important risk factors for the emergence and transmission of antimicrobial resistance. Most studies found that worse socioeconomic indicators were associated with higher rates of antimicrobial resistance. Our analysis showed an overall antimicrobial resistance rate of 32.5%, with the highest rates for S. aureus (40.6%) and the lowest for E. coli (25.7%). We found a small but consistent negative association between socioeconomic factors (income, education, and occupation) and overall antimicrobial resistance in univariate (p < 0.01) and multivariate analyses (p < 0.01), driven by resistant P. aeruginosa and S. aureus.

Conclusion.

Socioeconomic factors beyond health care and hospital settings may affect the emergence and dissemination of antimicrobial resistance. Preventing and controlling antimicrobial resistance requires efforts above and beyond reducing antibiotic consumption.

Profile of Enterobacteria Resistant to Beta-Lactams

A serious emerging problem worldwide is increased antimicrobial resistance. Acquisition of coding genes for evasion methods of antimicrobial drug mechanisms characterizes acquired resistance. This phenomenon has been observed in Enterobacteriaceae family. Treatment for bacterial infections is performed with antibiotics, of which the most used are beta-lactams. The aim of this study was to correlate antimicrobial resistance profiles in Enterobacteriaceae by phenotypic methods and molecular identification of 14 beta-lactamase coding genes. In this study, 70 exclusive isolates from Brazil were used, half of which were collected in veterinary clinics or hospitals Phenotypic methodologies were used and real-time PCR was the molecular methodology used, through the Sybr Green system. Regargding the results found in the tests it was observed that 74.28% were resistant to ampicillin, 62.85% were resistant to amoxicillin associated with clavalunate. The mechanism of resistance that presented the highest expression was ESBL (17.14%). The genes studied that were detected in a greater number of species were blaGIM and blaSIM (66.66% of the samples) and the one that was amplified in a smaller number of samples was blaVIM (16.66%). Therefore, high and worrying levels of antimicrobial resistance have been found in enterobacteria, and a way to minimize the accelerated emergence of their resistance includes developing or improving techniques that generate diagnoses with high efficiency and speed.

Analysis of Resistance Gene Prevalence in Whole-Genome Sequenced Enterobacteriales from Brazil

Enterobacteriales is an order of bacteria responsible for community and hospital-acquired infections related to high rates of antimicrobial resistance and increased treatment costs, morbidity, and mortality globally. The aims of this study were to analyze the frequency of the resistance genes detected and distribution over the years and sources of isolation in sequenced Enterobacteriales strains isolated in Brazil and available at the Pathogen Detection website. The presence of resistance genes was analyzed in 1,507 whole-genome sequenced strains of 19 Enterobacteriales species. A total of 58.0% of the strains presented resistance genes to at least one antimicrobial class and 684 strains presented a multidrug-resistant (MDR) profile. Resistance genes to 14 classes of antimicrobials were detected. Aminoglycosides presented the most prevalent and diverse resistance genes, while the sulfonamide resistance gene, sul2, was the most prevalent among the strains studied. The presence of resistance genes from 14 different antimicrobial classes, the high levels of MDR strains, and the detection of genes related to clinical and veterinary-used drugs reinforce the necessity of more efficient control measures. Moreover, it warns for the necessity of the rational use of antimicrobials in veterinary and clinical situations in Brazil, since contaminated food may act as a vehicle for human infections.

Diversity of clonal types of Klebsiella pneumoniae causing infections in intensive care neonatal patients in a large urban setting

BACKGROUND

Klebsiella infections are reported from neonatal intensive care units (NICUs) worldwide, but data on their incidence and genetic diversity remain scarce.

OBJECTIVE

We determined the incidence and genetic diversity of Klebsiella infections in NICU patients in Rio de Janeiro.

METHODS

This was a prospective study including newborns admitted to NICU in three hospitals during April 2005-November 2006 and March 2008-February 2009. Klebsiella pneumoniae isolates were genotyped by multilocus sequence typing (MLST) and extended spectrum β-lactamases (ESBL) were characterized.

RESULTS

Klebsiella infections occurred in 38 of 3984 patients (incidence rate, 9.5/1000 admissions); 14 (37%) of these 38 newborns died. Two clonal groups, CC45 and CC1041, caused 11 cases (42% of K. pneumoniae infection). Ten (32%) of the isolates causing infection produced ESBL, 9 of which (83%) carried bla_CTX-M-15, all belonging to clonal complex (CC) 45 and CC1041. Nine of these ESBL-producing isolates were confined to only one of the NICUs.

MAJOR CONCLUSIONS

The high incidence of Klebsiella infections in NICU in Rio de Janeiro appeared to be due to a combination of frequent sporadic infections caused by multiple K. pneumoniae genotypes and small outbreaks caused by dominant multidrug-resistant clones.

Characterization and whole genome sequencing of closely related multidrug-resistant Salmonella enterica serovar Heidelberg isolates from imported poultry meat in the Netherlands

Multidrug-resistant Salmonella enterica serovar Heidelberg isolates are frequently recovered in the Netherlands from poultry meat imported from South America. Our aim was to retrospectively assess the characteristics of the antimicrobial determinants, gene content and the clonal relatedness of 122 unique S. Heidelberg isolates from chicken meat from Brazil (n = 119) and Argentina (n = 3) that were imported between 2010 and 2015. These isolates were subjected to antimicrobial susceptibility testing, PCR and Illumina HiSeq2500 whole genome sequencing. Draft genomes were assembled to assess the gene content, and the phylogenetic relationships between isolates were determined using single nucleotide polymorphisms. Ciprofloxacin-resistance was identified in 98.4% of the isolates and 83.7% isolates showed resistance to the extended-spectrum cephalosporins cefotaxime and ceftazidime (83.6% and 82.8% respectively). Of the latter, 97.1% exhibited an AmpC phenotype and contained blaCMY-2, whereas the remaining three isolates contained an extended spectrum beta-lactamase. Of the 99 extended-spectrum cephalosporins-resistant isolates harboring CMY-2 plasmids, 56.6% contained the incompatibility group I1 replicon. Phylogenetic cluster analysis showed that all isolates from Brazil clustered together, with 49% occurring in clusters larger than 5 isolates that revealed intra-cluster similarities based on geographical location and/or resistance profiles. The remaining isolates were classified in smaller clusters or as singletons, highlighting the large diversity of S. Heidelberg in the poultry chain in Brazil that was revealed by this study. Considering the potential public health risk associated with multidrug-resistant S. Heidelberg in imported poultry, collaborative whole genome sequencing-based surveillance is needed to monitor the spread, pathogenic properties and epidemiological distribution of these isolates.

Bloodstream infections caused by multidrug-resistant gram-negative bacteria: epidemiological, clinical and microbiological features

Background

Bloodstream infections (BSI) are associated with high morbidity and mortality. This scenario worsens with the emergence of drug-resistant pathogens, resulting in infections which are difficult to treat or even untreatable with conventional antimicrobials. The aim of this study is to describe the epidemiological aspects of BSI caused by multiresistant gram-negative bacilli (MDR-GNB).

Methods

We conducted a laboratory-based surveillance for gram-negative bacteremia over a 1-year period. The bacterial isolates were identified by MALDI-TOF/MS and the antimicrobial susceptibility testing was performed by VITEK®2. Resistance genes were identified through PCR assays.

Results

Of the 143 patients, 28.7% had infections caused by MDR-GNB. The risk factors for MDR bacteremia were male sex, age ≥ 60, previous antimicrobial use, liver disease and bacteremia caused by K. pneumoniae. K. pneumoniae was the most frequently observed causative agent and had the highest resistance level. Regarding the resistance determinants, SHV, TEM, OXA-1-like and CTX-M-gp1 were predominant enzymatic variants, whereas CTX-M-gp9, CTX-M-gp2, KPC, VIM, GES, OXA-48-like, NDM and OXA-23-like were considered emerging enzymes.

Conclusions

Here we demonstrate that clinically relevant antibiotic resistance genes are prevalent in this setting. We hope our findings support the development of intervention measures by policy makers and healthcare professionals to face antibiotic resistance.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4265-z) contains supplementary material, which is available to authorized users.

Detection of multidrug-resistant Enterobacteriaceae isolated from river waters flowing to the Guanabara Bay and from clinical samples of hospitals in Rio de Janeiro, Brazil

INTRODUCTION

The use of antibiotics in humans, animal husbandry and veterinary activities induces selective pressure leading to the colonization and infection by resistant strains.

OBJECTIVE

We evaluated water samples collected from rivers of the Guanabara Bay, which have suffered minor and major environmental degradation, and clinical samples of hospital origin to detect evidence of the presence of resistance genes to aminoglycosides, beta-lactam antibiotics and fluoroquinolones in strains of Klebsiella pneumoniae subsp. pneumoniae, K. pneumoniae subsp. ozaenae and Escherichia coli.

MATERIALS AND METHODS

For isolation of the water strains we employed culture media containing 32 μg/ml cephalotin and 8 μg/ml gentamicin. The strains from clinical materials were selected using culture media containing 8 μg/ml gentamicin. The strains were identified and subjected to antimicrobial susceptibility testing (AST), plasmid DNA extraction and polymerase chain reaction (PCR) to detect genes encoding enzymes modifying aminoglycosides (EMA), extended-spectrum beta-lactamases (ESBL) and plasmid mechanisms of quinolone resistance (PMQR).

RESULTS

The AST of the isolates recovered from water samples showed multidrugresistance profiles similar to those found in isolates recovered from clinical materials. All isolates from water samples and 90% of the isolates from clinical samples showed at least one plasmid band. In the PCR assays, 7.4% of the isolates recovered from water samples and 20% of those from clinical materials showed amplification products for the three antimicrobial classes.

CONCLUSION

We believe that the detection of microorganisms presenting genetic elements in environments such as water is necessary for the prevention and control of their dissemination with potential to infect humans and other animals in eventual contact with these environments.

Individual- and community-level risk factors for ESBL Enterobacteriaceae colonization identified by universal admission screening in London

OBJECTIVES

We evaluated risk factors for gastrointestinal carriage of Enterobacteriaceae which produce extended-spectrum β-lactamases (ESBL-E), including individual-level variables such as antibiotic use and foreign travel, and community-level variables such as housing and deprivation.

METHODS

In an observational study in 2015, all patients admitted to a London hospital group were approached to be screened for ESBL-E carriage using rectal swabs for 4 months. Patients completed a risk factor questionnaire. Those with a residential postcode in the local catchment area were linked to a database containing community-level risk factor data. Risk factors for ESBL-E carriage were determined by binary logistic regression.

RESULTS

Of 4006 patients, 360 (9.0%) carried ESBL-E. Escherichia coli was the most common organism (77.8%), and CTX-M-type ESBLs were the most common genes (57.9% CTX-M-15 and 20.7% CTX-M-9). In multivariable analysis, risk factors for phenotypic ESBL-E among the 1633 patients with a residential postcode within the local catchment area were: travel to Asia (OR 4.4, CI 2.5-7.6) or Africa (OR 2.4, CI 1.2-4.8) in the 12 months prior to admission, two or more courses of antibiotics in the 6 months prior to admission (OR 2.0, CI 1.3-3.0), and residence in a district with a higher-than-average prevalence of overcrowded households (OR 1.5, CI 1.05-2.2). .

CONCLUSIONS

Both individual and community variables were associated with ESBL-E carriage at hospital admission. The novel observation that household overcrowding is associated with ESBL-E carriage requires confirmation, but raises the possibility that targeted interventions in the community could help prevent transmission of antibiotic-resistant Gram-negative bacteria.

Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil

Urinary tract infections (UTIs) are often caused by Escherichia coli. Their increasing resistance to broad-spectrum antibiotics challenges the treatment of UTIs. Whereas, E. coli ST131 is often multidrug resistant (MDR), ST69 remains susceptible to antibiotics such as cephalosporins. Both STs are commonly linked to community and nosocomial infections. E. coli phylogenetic groups B2 and D are associated with virulence and resistance profiles making them more pathogenic. Little is known about the population structure of E. coli isolates obtained from urine samples of hospitalized patients in Brazil. Therefore, we characterized E. coli isolated from urine samples of patients hospitalized at the university and three private hospitals in Rio de Janeiro, using whole genome sequencing. A high prevalence of E. coli ST131 and ST69 was found, but other lineages, namely ST73, ST648, ST405, and ST10 were also detected. Interestingly, isolates could be divided into two groups based on their antibiotic susceptibility. Isolates belonging to ST131, ST648, and ST405 showed a high resistance rate to all antibiotic classes tested, whereas isolates belonging to ST10, ST73, ST69 were in general susceptible to the antibiotics tested. Additionally, most ST69 isolates, normally resistant to aminoglycosides, were susceptible to this antibiotic in our population. The majority of ST131 isolates were ESBL-producing and belonged to serotype O25:H4 and the H30-R subclone. Previous studies showed that this subclone is often associated with more complicated UTIs, most likely due to their high resistance rate to different antibiotic classes. Sequenced isolates could be classified into five phylogenetic groups of which B2, D, and F showed higher resistance rates than groups A and B1. No significant difference for the predicted virulence genes scores was found for isolates belonging to ST131, ST648, ST405, and ST69. In contrast, the phylogenetic groups B2, D and F showed a higher predictive virulence score compared to phylogenetic groups A and B1. In conclusion, despite the diversity of E. coli isolates causing UTIs, clonal groups O25:H4-B2-ST131 H30-R, O1:H6-B2-ST648, and O102:H6-D-ST405 were the most prevalent. The emergence of highly virulent and MDR E. coli in Brazil is of high concern and requires more attention from the health authorities.

Seasonal variation of macrolide resistance gene abundances in the South Fork Iowa River Watershed

The Midwestern United States is dominated by agricultural production with high concentrations of swine, leading to application of swine manure onto lands with artificial subsurface drainage. Previous reports have indicated elevated levels of antibiotic resistance genes (ARGs) in surface water and groundwater around confined animal feeding operations which administer antimicrobials. While previous studies have examined the occurrence of ARGs around confined swine feeding operations, little information is known how their transport from tile-drained fields receiving swine manure application impacts downstream environments. To further our knowledge in this area, water samples were collected from five locations in the agriculturally dominated South Fork Iowa River Watershed with approximately 840,000 swine present in the 76,000ha basin. Samples were collected monthly from three stream sites and two main artificial subsurface drainage outlets. Samples were analyzed for macrolide resistance genes ermB, ermF and 16S rRNAgene abundance using qPCR. Abundance of erm genes ranged from below limits of quantification to >10⁷ copies 100mL^-1 water. Eighty-nine percent of stream water samples contained one of these two ARGs. Results indicate significantly more ermB and ermF in main drainage outlets than stream samples when normalized by 16S rRNA abundance (p<0.0001). Both artificial drainage locations revealed temporal trends for ermB and ermF abundance when normalized to 16S rRNA abundance. The higher resistance gene concentrations identified in artificial drainage samples occurring mid-Spring and late-Fall are likely due to manure application.

Genetic Background of β-Lactamases in Enterobacteriaceae Isolates from Environmental Samples

The prevalence of β-lactamase-producing Enterobacteriaceae has increased worldwide. Although antibiotic-resistant bacteria are usually associated with hospitals, there are a growing number of reports of resistant bacteria in other environments. Concern about resistant microorganisms outside the hospital setting highlights the need to investigate mechanisms of antibiotic resistance in isolates collected from the environment. The present study evaluated the resistance mechanism to β-lactam antibiotics in 40 isolates from hospital sewage and surface water from the Dilúvio Stream, Porto Alegre City, Southern Brazil. The multiplex PCR technique was used to detect several resistance genes of β-lactamases: extended-spectrum β-lactamases (ESBLs), carbapenemases, and β-lactamase AmpC. After genes, detection amplicons were sequenced to confirm their identification. The clonal relationship was established by DNA macrorestriction using the XbaI enzyme, followed by pulsed-field gel electrophoresis (PFGE). The results indicated that resistance genes were present in 85% of the isolates. The most prevalent genes encoded narrow-spectrum β-lactamase, such as TEM-1 and SHV-1 with 70% of the strains, followed by carbapenemase KPC and GES (45%), ESBL types SHV-5 and CTX-M-8 (27.5%), and AmpC (ACT-1/MIR-1) (2.5%). Twelve isolates contained only one resistance gene, 14 contained two, and eight isolates had three resistance genes. PFGE indicated a clonal relationship among K. pneumoniae isolates. It was not possible to establish a clonal relationship between Enterobacter sp. isolates. The results highlight the potential of these resistance genes to spread in the polluted environment and to present a health risk to communities. This report is the first description of these resistance genes present in environmental samples other than a hospital in the city of Porto Alegre/RS.

Detection of molecular changes induced by antibiotics in Escherichia coli using vibrational spectroscopy

This study aimed to test Raman (400-1800cm^-1) and Infra-red (1900-500cm^-1) spectroscopies followed by statistical analysis (principal component analysis) to detect molecular changes induced by antibiotics (ampicillin, cefotaxime - cell wall synthesis inhibitors, tetracycline - protein synthesis inhibitor, ciprofloxacin - DNA synthesis inhibitor) against Escherichia coli TOP10. In case of ampicillin and cefotaxime, a decrease in protein bands in both Raman (1240, 1660cm^-1), and IR spectra (1230, 1530, 1630cm^-1), and an increase in carbohydrate bands (1150, 1020cm^-1) in IR spectra were observed. Tetracycline addition caused an increase in nucleic acid bands (775, 1478, 1578cm^-1), a sharp decrease in phenylalanine (995cm^-1) in Raman spectra and the amide I and amide II bands (1630, 1530cm^-1) in IR spectra, an increase in DNA in both Raman (1083cm^-1) and IR spectra (1080cm^-1). Regarding ciprofloxacin, an increase in nucleic acids (775, 1478, 1578cm^-1) in Raman spectra and in protein bands (1230, 1520, 1630cm^-1), in DNA (1080cm^-1) in IR spectra were detected. Clear discrimination of antibiotic-treated samples compared to the control was recorded, showing that Raman and IR spectroscopies, coupled to principal component analysis for data, could be used to detect molecular modifications in bacteria exposed to different classes of antibiotics. These findings contribute to the understanding of the mechanisms of action of antibiotics in bacteria.

Geographical variation in therapy for bloodstream infections due to multidrug-resistant Enterobacteriaceae: a post-hoc analysis of the INCREMENT study

We describe regional differences in therapy for bloodstream infection (BSI) caused by extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) or carbapenemase-producing Enterobacteriaceae (CPE). Patients (n = 1482) in 12 countries from an observational study of BSI caused by ESBL-E or CPE were included. Multivariate logistic regression was used to calculate adjusted odds ratios (aORs) for the influence of country of recruitment on empirical use of β-lactam/β-lactamase inhibitors (BLBLIs) or carbapenems, targeted use of BLBLIs for ESBL-E and use of targeted combination therapy for CPE. Compared with Spain, BLBLI use for empirical therapy was least likely in sites from Israel (aOR 0.34, 95% CI 0.14-0.81), Greece (aOR 0.49, 95% CI 0.26-0.94) and Canada (aOR 0.31, 95% CI 0.11-0.88) but more likely in Italy (aOR 1.58, 95% CI 1.11-2.25) and Turkey (aOR 2.09, 95% CI 1.14-3.81). Empirical carbapenem use was more likely in sites from Taiwan (aOR 1.73, 95% CI 1.03-2.92) and USA (aOR 1.89, 95% CI 1.05-3.39) and less likely in Italy (aOR 0.44, 95% CI 0.28-0.69) and Canada (aOR 0.10, 95% CI 0.01-0.74). Targeted BLBLIs for ESBL-E was more likely in Italian sites. Treatment at sites within Israel, Taiwan, Turkey and Brazil was associated with less combination therapy for CPE. Although this study does not provide precise data on the relative prevalence of ESBL-E or CPE, significant variation in therapy exists across countries even after adjustment for patient factors. Better understanding of what influences therapeutic choices for these infections will aid antimicrobial stewardship efforts.

Evidence of antibiotic resistance in Enterobacteriales isolated from green sea turtles, Chelonia mydas on the Great Barrier Reef

This study investigated Enterobacteriales and their antimicrobial resistance in green sea turtles captured adjacent to the central Great Barrier Reef (GBR) and proximate to urban development. Cloacal swabs were taken from 73 green turtles between 2015 and 2016. A total of 154 out of 341 Gram-negative bacterial isolates were identified as Enterobacteriales that represent 16 different species from 9 different genera. The dominant isolates were Citrobacter (30.52%), Edwardsiella (21.43%) and Escherichia (12.34%). The resistance against 12 antibiotics belonging to 6 different classes was determined. The isolates showed highest resistance to β-lactam antibiotics (78.57%) followed by quinolone (50%) and tetracycline classes (46.1%). Approximately one-third (37.7%) of the isolates identified exhibited multidrug-resistance. Isolates recovered from rehabilitated turtles were significantly multidrug resistant (p<0.009) compared to isolates from other study sites. These results provide baseline information on antimicrobial resistance while revealing gaps for further research to evaluate the level of pollution in the GBR.

Carbapenem-Resistant Enterobacteriaceae: A Strategic Roadmap for Infection Control

The incidence of carbapenem-resistant Enterobacteriaceae (CRE) has increased worldwide with great regional variability. Infections caused by these organisms are associated with crude mortality rates of up to 70%. The spread of CRE in healthcare settings is both an important medical problem and a major global public health threat. All countries are at risk of falling victim to the emergence of CRE; therefore, a preparedness plan is required to avoid the catastrophic natural course of this epidemic. Proactive and adequate preventive measures locally, regionally, and nationally are required to contain the spread of these bacteria. The keys to success in preventing the establishment of CRE endemicity in a region are early detection through targeted laboratory protocols and containment of spread through comprehensive infection control measures. This guideline provides a strategic roadmap for infection control measures based on the best available evidence and expert opinion, to enable preparation of a multifaceted preparedness plan to abort epidemics of CRE. Infect Control Hosp Epidemiol 2017;38:580-594.

Drug-resistance dynamics of Staphylococcus aureus between 2008 and 2014 at a tertiary teaching hospital, Jiangxi Province, China

Background

To understand the relationship between the Staphylococcus aureus infection rate and the reasonable usage of antibiotics, which will help in the effective control of MRSA infection.

Methods

All data were obtained by the application of the nosocomial infection surveillance network. Drug resistance, departmental sources, and isolated sites as well as infection rate variations of S. aureus were analyzed in the 7-year period in key departments.

Results

Between 2008 and 2014, 2525 strains of S. aureus isolates, mainly from sputum, skin/soft tissue, bloodstreams were collected from several hospital departments including respiratory, burn, brain surgery, orthopedics, ICU, and emergency. During these periods, the resistance rate of S. aureus to most drugs, including oxacillin, tetracycline, erythromycin, clindamycin, gentamicin, and ciprofloxacin, showed a tendency to decrease. The resistance to sulphamethoxazole/trimethoprim showed the opposite trend (P = 0.075) and there were no S. aureus strains resistant to linezolid and vancomycin. The MRSA infection rate was different across crucial hospital departments, with the burns department and ICU maintaining a high infection level. Over the 7-year period, both the brain surgery and the emergency departments had an expected upward trend (P < 0.05), while the orthopedic department showed a clear downward trend (P < 0.05) in MRSA infection rate.

Conclusion

Hospitals should continue to maintain the current pattern of antibiotic administration, while more effective measures should be taken to reduce the high MRSA infection rate in some important hospital departments.

Detection and molecular characterization of β-lactamase genes in clinical isolates of Gram-negative bacteria in Southern Ecuador

This work performed a phenotypic and genotypic characterization of 79 clinical isolates of Enterobacteriaceae and Pseudomonadaceae collected in hospitals of Southern Ecuadorin 2013. Our results showed a high incidence of β-lactamases and ESBLs with bla_TEM and bla_CTX-M as the prevalent genes, respectively. By direct sequencing of PCR amplicons, the different β-lactamases and variants of the genes were also distinguished. Our results revealed a predominance of TEM-1 β-lactamase and the presence of different CTX-M variants with a prevalence of CTX-M-15. Two infrequent CTX-M variants in South America were also identified. To the best of our knowledge, this is one of the first studies describing the genetic characteristics of β-lactamases in Ecuador.

Characterization of the variable region in the class 1 integron of antimicrobial-resistant Escherichia coli isolated from surface water

Fecal bacteria are considered to be a potential reservoir of antimicrobial resistance genes in the aquatic environment and could horizontally transfer these genes to autochthonous bacteria when carried on transferable and/or mobile genetic elements. Such circulation of resistance genes constitutes a latent public health hazard. The aim of this study was to characterize the variable region of the class 1 integron and relate its genetic content to resistance patterns observed in antimicrobial-resistant Escherichia coli isolated from the surface waters of Patos Lagoon, Southern Brazil. Genetic diversity of the isolates and presence of the qacEΔ1 gene, which confers resistance to quaternary ammonium compounds, were also investigated. A total of 27 isolates were analyzed. The variable region harbored dfrA17, dfrA1 and dfrA12 genes, which confer resistance to trimethoprim, and aadA1, aadA5 and aadA22 genes that encode resistance to streptomycin/spectinomycin. Most of the isolates were considered resistant to quaternary ammonium compounds and all of them carried the qacEΔ1 gene at the 3′ conserved segment of the integron. ERIC-PCR analyses of E. coli isolates that presented the integrons showed great genetic diversity, indicating diverse sources of contamination in this environment. These results suggest that fecal bacteria with class 1 integrons in aquatic environments are potentially important reservoirs of antibiotic-resistance genes and may transfer these elements to other bacteria that are capable of infecting humans.

Occurrence and characteristics of extended spectrum beta-lactamases-producing Enterobacteriaceae from foods of animal origin

Presence of extended spectrum beta-lactamases (ESBL) in bacteria is a growing health concern of global significance. The local, regional, national, and international epidemiological studies for extended spectrum beta-lactamases-producing Enterobacteriaceae and their encoding genes in foods are still incomplete. The objective of this study was to determine the occurrence of extended spectrum beta-lactamases-producing Enterobacteriaceae and the characteristics of their encoding genes from a total of 250 samples of various foods of animal-origin (100 raw chicken meat, 100 raw cow milk, and 50 raw cow milk cheese) sold in Turkey. Overall, 55 isolates were positive as extended spectrum beta-lactamases-producing Enterobacteriaceae. The most prevalent extended spectrum beta-lactamases-producing strain were identified as Escherichia coli (80%), followed by Enterobacter cloacae (9.1%), Citrobacter braakii (5.5%), Klebsiella pneumoniae (3.6%), and Citrobacter werkmanii (1.8%) by Vitek^® MS. The simultaneous production of extended spectrum beta-lactamases and AmpC was detected in five isolates (9.1%) in E. coli (80%) and E. cloacae (20%). The frequency rates of bla_TEM, bla_CTX-M, and bla_SHV were 96.4%, 53.7%, and 34.5%, respectively. The co-existence of bla-genes was observed in 82% of extended spectrum beta-lactamases producers with a distribution of bla_TEM & bla_CTX-M (52.7%), bla_TEM & bla_SHV (20%), bla_TEM & bla_CTX-M & bla_SHV (12.7%), and bla_SHV & bla_CTX-M (1.8%). The most prevalent variant of bla_CTX-M clusters was defined as bla_CTX-M-1 (97.2%), followed by bla_CTX-M-8 (2.8%). In summary, the analysed foods were found to be posing a health risk for Turkish consumers due to contamination by Enterobacteriaceae with a diversity of extended spectrum beta-lactamases encoding genes.

Antimicrobial susceptibility and emerging resistance determinants (blaCTX-M, rmtB, fosA3) in clinical isolates from urinary tract infections in the Bolivian Chaco

BACKGROUND

Bolivia is among the lowest-resourced South American countries, with very few data available on antibiotic resistance in bacterial pathogens. The phenotypic and molecular characterization of bacterial isolates responsible for urinary tract infections (UTIs) in the Bolivian Chaco are reported here.

METHODS

All clinical isolates from UTIs collected in the Hospital Basico Villa Montes between June 2010 and January 2014 were analyzed (N=213). Characterization included susceptibility testing, extended-spectrum beta-lactamase (ESBL) detection, identification of relevant resistance determinants (e.g., CTX-M-type ESBLs, 16S rRNA methyltransferases, glutathione S-transferases), and genotyping of CTX-M producers.

RESULTS

Very high resistance rates were observed. Overall, the lowest susceptibility was observed for trimethoprim-sulphamethoxazole, tetracycline, nalidixic acid, amoxicillin-clavulanic acid, ciprofloxacin, and gentamicin. Of E. coli and K. pneumoniae, 11.6% were ESBL producers. Resistance to nitrofurantoin, amikacin, and fosfomycin remained low, and susceptibility to carbapenems was fully preserved. CTX-M-15 was the dominant CTX-M variant. Four E. coli ST131 (two being H30-Rx) were identified. Of note, isolates harbouring rmtB and fosA3 were detected.

CONCLUSIONS

Bolivia is not an exception to the very high resistance burden affecting many South American countries. Optimization of alternative approaches to monitor local antibiotic resistance trends in resource-limited settings is strongly encouraged to support the implementation of effective empiric treatment guidelines.

Risk factors for and impact of carbapenem-resistant Acinetobacter baumannii colonization and infection: matched case-control study

The objective of this investigation was to identify risk factors for carbapenem-resistant Acinetobacter baumannii (CRAB) and its association with mortality. A population-based matched case-control study using the computerized database of Clalit Health Services (CHS) in the period between 2007 and 2012 was conducted. Hospitalized patients with CRAB colonization or infection were compared to hospitalized patients without evidence of A. baumannii, matched by age, ward of hospitalization, season, Charlson score, and length of hospitalization. Risk factors for CRAB isolation were searched for using multivariate analysis. Association of CRAB and other risk factors with mortality were assessed in the cohort. A total of 1190 patients with CRAB were matched to 1190 patients without CRAB. Low socioeconomic status was independently associated with CRAB isolation and CRAB bacteremia [odds ratio 2.18, 95% confidence interval (CI) 1.02-5]. Other risk factors were invasive procedures and bacteremia with other pathogens prior to CRAB isolation, and various comorbidities. Among all patients, CRAB isolation was independently associated with increased mortality (hazard ratio 2.33, 95% CI 2.08-2.6). Socioeconomic status is associated with health outcomes. Our population-based study revealed an almost doubled risk for CRAB in patients at lower socioeconomic status and an association with healthcare exposure. CRAB was associated with mortality and might become a risk indicator for complex morbidity and mortality.