Prolonged Outbreak of Carbapenem and Colistin-Resistant Klebsiella pneumoniae at a Large Tertiary Hospital in Brazil.

Multidrug-resistant gram-negative bacteria, such as carbapenem and colistin-resistant Klebsiella pneumoniae (ColR-CRKP), represent a major problem for health systems worldwide and have high lethality. This study investigated the genetic relationship, antimicrobial susceptibility profile, and resistance mechanisms to ColR-CRKP isolates from patients infected/colonized in a tertiary hospital in Salvador, Bahia/Brazil. From September 2016 to January 2018, 46 patients (56 ColR-CRKP positive cultures) were enrolled in the investigation but clinical and demographic data were obtained from 31 patients. Most of them were men (67.7%) and elderly (median age of 62 years old), and the median Charlson score was 3. The main comorbidities were systemic arterial hypertension (38.7%), diabetes (32.2%), and cerebrovascular disease (25.8%). The average hospitalization stay until ColR-CRKP identification in days were 35.12. A total of 90.6% used mechanical ventilation and 93.7% used a central venous catheter. Of the 31 patients who had the data evaluated, 12 had ColR-CRKP infection, and seven died (58.4%). Previous use of polymyxins was identified in 32.2% of the cases, and carbapenems were identified in 70.9%. The minimum inhibitory concentration (MIC) for colistin was > 16 µg/mL, with more than half of the isolates (55%) having a MIC of 256 µg/mL. The bla KPC gene was detected in 94.7% of the isolates, bla NDM in 16.0%, and bla GES in 1.7%. The bla OXA-48, bla VIM, and bla IMP genes were not detected. The mcr-1 test was negative in all 56 isolates. Alteration of the mgrB gene was detected in 87.5% (n = 49/56) of the isolates, and of these, 49.0% (24/49) had alteration in size probably due to IS903B, 22.4% (11/49) did not have the mgrB gene detected, 20.4% (10/49) presented the IS903B, 6.1% (3/49) had a premature stop codon (Q30*), and 2.1% (1/49) presented a thymine deletion at position 104 - 104delT (F35fs). The PFGE profile showed a monoclonal profile in 84.7% of the isolates in different hospital sectors, with ST11 (CC-258) being the most frequent sequence type. This study presents a prolonged outbreak of ColR-CRKP in which 83.9% of the isolates belonged to the same cluster, and 67.6% of the patients evaluated had not used polymyxin, suggesting the possibility of cross-transmission of ColR-CRKP isolates.

High levels of gut carriage of antimicrobial-resistant Escherichia coli in community settings in Rio de Janeiro, Brazil.

The prevalence and risk factors for gut carriage of antimicrobial-resistant Escherichia coli among individuals living in the community in Rio de Janeiro, Brazil, are unknown. The aim of this study was to determine the prevalence of colonization with antimicrobial-resistant E. coli, including isolates producing ESBL and harboring plasmid-mediated quinolone resistant (PMQR) genes in this community. We performed a cross-sectional study and analyzed fecal specimens of individuals attending outpatient clinics in the city from January 2015 to July 2019. We investigated susceptibility to antimicrobial agents by disc diffusion tests and used PCR to determine ESBL types, PMQR, and the virulence genes that characterize an isolate as extraintestinal pathogenic E. coli (ExPEC). Among the 623 subjects, 212 (34%) carried an isolate resistant to at least one of the tested antimicrobial agents, with the highest frequencies of resistance to ampicillin (26%), trimethoprim-sulfamethoxazole (19%), cefazolin (14%), and ciprofloxacin (CIP, 9%). In addition, 13% (81) of subjects carried a multidrug-resistant-E. coli (MDR-E), including 47 (8% of all isolates) ESBL-producing E. coli (ESBL-E), mainly of CTX-M-8 (15, 32%) and CTX-M-15 (9, 20%) types. PMQR genes were present in 7% (42) of all isolates, including 60% (32) of the 53 resistant to CIP. Previous use of antimicrobial agents, particularly fluoroquinolones, was a risk factor for colonization with MDR-E (25%, 20/81 vs 13%, 70/542, p = 0.01), ESBL-E (28%, 13/47, vs 13%, 77/576, p = 0.01), and resistance to CIP (26%, 14/53, vs 12%, 70/570, p = 0.01). The most pathogenic phylogroups B2, C, and D were 37% of the MDR-E, 30% of the ESBL-E, 38% of the CIP-resistant, and 31% of PMQR gene carrying E. coli isolates. We show that carriage of MDR-E (mostly ESBL-E) reached high levels in the community in Rio de Janeiro, increased by the selection of antimicrobial agents. Much of the resistant E. coli isolates are potential pathogenic strains. The widespread use of antimicrobial agents during the COVID-19 pandemic in Brazil may have worsened this picture.

OXA-181 carbapenemase carried on an IncX3 plasmid in high-risk Escherichia coli ST167 isolated from a traveler returning from Sub-Saharan Africa to Brazil.

This is the first detection and genomic analysis of an OXA-181-carbapenemase-producing E. coli in Brazil, from a traveler returning from Sub-Saharan Africa. The ST167 isolate carries blaOXA-181 inserted in an IncX3 plasmid. This report illustrates the potential role of travelers as silent vectors for dissemination of high-risk resistant clones.

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 blaCTX-M-15 carrying Escherichia coli. One traveler acquired one isolate carrying blaOXA-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.

Prevalence of fluoroquinolone-resistant and broad-spectrum cephalosporin-resistant community-acquired urinary tract infections in Rio de Janeiro: Impact of Escherichia coli genotypes ST69 and ST131.

Uropathogenic Escherichia coli (UPEC) is the leading cause of community-acquired urinary tract infection (CA-UTI). The increasing prevalence of CA-UTI caused by UPEC strains resistant to broad-spectrum drugs complicates clinical management of these infections. Here we assessed the prevalence of antimicrobial drug resistance, genotypes and beta-lactamase genes among UPEC isolated from cases of CA-UTI in Rio de Janeiro, Brazil during November 2015 to determine if the prevalence of drug-resistant CA-UTI is determined by multiple genotypes of resistant UPEC or dissemination of key lineages of UPEC. Among 499 UPEC isolates, 98 (20%) were ciprofloxacin (CIP) resistant and 41 (8%) produced extended-spectrum beta-lactamase (ESBL). Sequence types (ST) 69 and 131 were the most common genotypes, representing 77 (15%) and 42 (8%) of all UPEC isolates, respectively. Of fluoroquinolone-resistant isolates, ST69 and ST131 together accounted for 57%, while of ESBL-producers, ST131 represented 21%. Only 5 (2%) of 255 susceptible isolates belonged to these STs (p < .001). blaCTX-M-15 was detected in 17 (42%) of the 41 ESBL-producing isolates. Comparison with a collection of UPEC isolates obtained a decade earlier from the same community showed that a large proportion (60% and 25%, respectively) of the increase in CA-UTI caused by fluoroquinolone-resistant and ESBL-producing UPEC appears to be due to just two pandemic lineages ST131 and ST69. These findings indicate that much of the prevalence of broad-spectrum drug-resistant CA-UTI in Rio de Janeiro is due to a limited set of pandemic lineages of UPEC circulating in the community instead of multiple genotypes selected by antimicrobial agents.

CTX-M- and pAmpC-Encoding Genes Are Associated with Similar Mobile Genetic Elements in Escherichia coli Isolated from Different Brands of Brazilian Chicken Meat.

In this study we characterized the genetic environment of blaCTX-M and blaCMY-2 genes carried by 46 Escherichia coli isolates obtained from 20 chicken carcasses produced by five different brands in Brazil, including exporters and antibiotic-free-certified producers, purchased between 2010 and 2014. Similar plasmids characterized according to size and incompatibility group (Inc) were identified in E. coli belonging to different MLST-ST collected, regardless of carcass brand or production system. Hybridization assays with transconjugant strains revealed that blaCMY-2 gene (n = 19) was located on 85 kb plasmids of IncB/O, IncI1, IncFIB, or nontypeable groups. blaCTX-M-8 (n = 9) was located on 90 kb IncI1 plasmids. blaCTX-M-2 (n = 14) was inserted in class 1 integrons and conjugated only by one isolate in a 125 kb IncP plasmid. blaCTX-M-15 (n = 1), rarely described in isolates from food-producing animals in South America, was characterized by whole genome sequencing of transconjugant; the gene was carried in a 49.3 kb IncX1 plasmid. Sequencing of bla gene-flanking regions indicated the association of these genes with previously described insertion sequences. These results suggest that conserved genetic environments are related to ESBL and pAmpC genes in the Brazilian chicken production chain.

A novel plasmid-encoded mcr-4.3 gene in a colistin-resistant Acinetobacter baumannii clinical strain.

OBJECTIVES: To identify the molecular mechanism of colistin resistance in an MDR Acinetobacter baumannii clinical strain isolated in 2008 from a meningitis case in Brazil. METHODS: Long- and short-read WGS was used to identify colistin resistance genes in A. baumannii strain 597A with a colistin MIC of 64 mg/L. MS was used to analyse lipid A content. mcr was cloned into pET-26b (+) and transformed into Escherichia coli BL21(λDE3)pLysS for analysis. RESULTS: A novel plasmid (pAb-MCR4.3) harbouring mcr-4.3 within a Tn3-like transposon was identified. The A. baumannii 597A lipid A MS spectra showed a main molecular ion peak at m/z=2034, which indicated the addition of phosphoethanolamine to the lipid A structure. E. coli BL21 transformed with pET-26b-mcr-4.3 gained colistin resistance with a colistin MIC of 8 mg/L. CONCLUSIONS: Colistin resistance in A. baumannii 597A was correlated with the presence of a novel plasmid-encoded mcr-4.3 gene.

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 ß-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 blaCTX-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.

High-Level Multidrug-Resistant Escherichia coli Isolates from Wild Birds in a Large Urban Environment.

Intensive clinical use of antibiotics together with inadequate sanitation in an urban environment may contribute to the dissemination of multidrug-resistant (MDR) bacteria in the community. Wild birds living in these areas may become colonized with such organisms and further disseminate these resistant bacteria. In this study, we examined Escherichia coli isolates from the intestine of wild birds in Rio de Janeiro, Brazil, for those expressing extended-spectrum beta-lactamase (ESBL), carbapenemase, and other drug resistances. We obtained 353 E. coli isolates from 112 birds admitted to three wildlife centers in Rio de Janeiro state, from July 2010 to December 2013. MDR isolates were found in 43 (38%) birds, including 14 carrying E. coli isolates that expressed ESBL. All ESBL-encoding genes were blaCTX-M type, and no carbapenemase-producing isolates were found. MDR isolates belonged to a variety of lineages. Multilocus sequence type clonal complexes 648 and 155 accounted for carriage in 9 (21%) of 43 birds with MDR isolates. The study birds were nonmigratory, and the bacteria obtained from them likely mirrored urban circulating genotypes. Altogether, these findings indicate a high level of environmental contamination with clinically relevant drug resistance genes in Rio de Janeiro. A large proportion of the MDR strains belonged to clonal lineages.

Preventing diseases in round-the-world travelers: a contemporary challenge for travel medicine advice.

Providing advice for travelers embarking on long-term trips poses a challenge in travel medicine. A long duration of risk exposure is associated with underuse of protective measures and poor adherence to chemoprophylaxis, increasing the chances of acquiring infections. Recently, in our clinic, we observed an increase in the number of travelers undertaking round-the-world trips. These individuals are typically aged around 32 years and quit their jobs to embark on one-to-two-year journeys. Their destinations include countries in two or more continents, invariably Southeast Asia and Indonesia, and mostly involve land travel and visiting rural areas. Such trips involve flexible plans, increasing the challenge, especially with regard to malaria prophylaxis. Advising round-the-world travelers is time-consuming because of the amount of information that must be provided to the traveler. Advisors must develop strategies to commit the traveler to his/her own health, and verify their learnings on disease-prevention measures. Contacting the advisor after the appointment or during the trip can be helpful to clarify unclear instructions or diagnosis made and prescriptions given abroad. Infectious diseases are among the most frequent problems affecting travelers, many of which are preventable by vaccines, medicines, and precautionary measures. The dissemination of counterfeit medicines, particularly antibiotics and antimalarial medicines, emphasizes the need for travelers to carry medicines that they may possibly need on their trip. Additional advice on altitude, scuba diving, and other possible risks may also be given. Considering the difficulties in advising this group, we present a review of the main recommendations on advising these travelers.

Preventing diseases in round-the-world travelers: a contemporary challenge for travel medicine advice

Abstract Providing advice for travelers embarking on long-term trips poses a challenge in travel medicine. A long duration of risk exposure is associated with underuse of protective measures and poor adherence to chemoprophylaxis, increasing the chances of acquiring infections. Recently, in our clinic, we observed an increase in the number of travelers undertaking round-the-world trips. These individuals are typically aged around 32 years and quit their jobs to embark on one-to-two-year journeys. Their destinations include countries in two or more continents, invariably Southeast Asia and Indonesia, and mostly involve land travel and visiting rural areas. Such trips involve flexible plans, increasing the challenge, especially with regard to malaria prophylaxis. Advising round-the-world travelers is time-consuming because of the amount of information that must be provided to the traveler. Advisors must develop strategies to commit the traveler to his/her own health, and verify their learnings on disease-prevention measures. Contacting the advisor after the appointment or during the trip can be helpful to clarify unclear instructions or diagnosis made and prescriptions given abroad. Infectious diseases are among the most frequent problems affecting travelers, many of which are preventable by vaccines, medicines, and precautionary measures. The dissemination of counterfeit medicines, particularly antibiotics and antimalarial medicines, emphasizes the need for travelers to carry medicines that they may possibly need on their trip. Additional advice on altitude, scuba diving, and other possible risks may also be given. Considering the difficulties in advising this group, we present a review of the main recommendations on advising these travelers.

Early prosthetic valve endocarditis caused by Corynebacterium amycolatum: the first case reported in Brazil.

Non-diphtheriae Corynebacterium species are usually considered as contaminants of clinical specimens due to their widely environmental distribution and colonization of the human skin and mucous membranes. However, these bacteria have been increasingly recognized as agents of life-threatening infections mainly in individuals in immunosuppressive conditions. These organisms have vast variation in morphology and biochemical reaction, characteristics that make the correct identification of Corynebacterium at the species level extremely difficult using conventional phenotypic methods. The precise identification of C. amycolatum requires approaches rarely available in conventional clinical microbiology laboratories, such as API Coryne system, 16s rRNA and rpoB gene sequencing. In this setting, MALDI-TOF, a quick, accurate, and relatively unexpansive molecular technique, arises as a cost-effective alternative for characterizing these agents. Here, a rare and lethal case of endocarditis caused by C. amycolatum is presented. This is the first case of infective endocarditis due to C. amycolatum reported in Brazil.

Antimicrobial resistance in Neisseria gonorrhoeae: history, molecular mechanisms and epidemiological aspects of an emerging global threat

ABSTRACT Neisseria gonorrhoeae is the agent of gonorrhea, a sexually transmitted infection with an estimate from The World Health Organization of 78 million new cases in people aged 15-49 worldwide during 2012. If left untreated, complications may include pelvic inflammatory disease and infertility. Antimicrobial treatment is usually effective; however, resistance has emerged successively through various molecular mechanisms for all the regularly used therapeutic agents throughout decades. Detection of antimicrobial susceptibility is currently the most critical aspect for N. gonorrhoeae surveillance, however poorly structured health systems pose difficulties. In this review, we compiled data from worldwide reports regarding epidemiology and antimicrobial resistance in N. gonorrhoeae, and highlight the relevance of the implementation of surveillance networks to establish policies for gonorrhea treatment.

Antimicrobial resistance in Neisseria gonorrhoeae: history, molecular mechanisms and epidemiological aspects of an emerging global threat.

Neisseria gonorrhoeae is the agent of gonorrhea, a sexually transmitted infection with an estimate from The World Health Organization of 78 million new cases in people aged 15-49 worldwide during 2012. If left untreated, complications may include pelvic inflammatory disease and infertility. Antimicrobial treatment is usually effective; however, resistance has emerged successively through various molecular mechanisms for all the regularly used therapeutic agents throughout decades. Detection of antimicrobial susceptibility is currently the most critical aspect for N. gonorrhoeae surveillance, however poorly structured health systems pose difficulties. In this review, we compiled data from worldwide reports regarding epidemiology and antimicrobial resistance in N. gonorrhoeae, and highlight the relevance of the implementation of surveillance networks to establish policies for gonorrhea treatment.

Staphylococcus saprophyticus Recovered from Humans, Food, and Recreational Waters in Rio de Janeiro, Brazil.

Staphylococcus saprophyticus is an important agent of urinary tract infection (UTI) in young women, but information about this pathogen in human microbiota and in common environment is lacking. The aim of this study was to characterize S. saprophyticus isolates from genitoanal microbiota of 621 pregnant women, 10 minas cheese packs, and five beaches in Rio de Janeiro city and compare PFGE profiles of these isolates with five UTI PFGE clusters described in this city. We investigated 65 S. saprophyticus isolates from microbiota, 13 from minas cheese, and 30 from beaches and 32 UTI isolates. Antimicrobial resistance was determined by disk diffusion, MIC by agar dilution, and PCR. Erythromycin-resistance genes erm(C), msr(A), msr(B), mph(C), and lin(A) were found in 93% of isolates. Trimethoprim-sulfamethoxazole resistance correlated with dfrG or dfrA genes. Three cefoxitin-resistant isolates carried the mecA gene. All isolates obtained from cheese were susceptible to all antimicrobial agents. Six of 10 pregnant women with >1 isolate had monoclonal colonization. Isolates from pregnant women shared 100% similarity with UTI PFGE cluster types A and E obtained almost 10 years previously, suggesting temporal persistence of S. saprophyticus. Antimicrobial resistance of beach isolates reflected the profiles of human isolates. Taken together, results indicate a shared source for human and environmental isolates.

The Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) identification versus biochemical tests: a study with enterobacteria from a dairy cattle environment

Abstract Mastitis adversely affects milk production and in general cows do not regain their full production levels post recovery, leading to considerable economic losses. Moreover the percentage decrease in milk production depends on the specific pathogen that caused the infection and enterobacteria are responsible for this greater reduction. Phenotypic tests are among the currently available methods used worldwide to identify enterobacteria; however they tend to misdiagnose the species despite the multiple tests carried out. On the other hand The Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) technique has been attracting attention for its precise identification of several microorganisms at species level. In the current study, 183 enterobacteria were detected in milk (n = 47) and fecal samples (n = 94) from cows, and samples from water (n = 23) and milk lines (n = 19). All these samples were collected from a farm in Rio de Janeiro with the specific purpose of presenting the MALDI-TOF MS technique as an efficient methodology to identify Enterobacteriaceae from bovine environments. The MALDI-TOF MS technique results matched the biochemical test results in 92.9% (170/183) of the enterobacteria species and the gyrB sequencing confirmed 100% of the proteomic technique results. The amino acid decarboxylation test made the most misidentifications and Enterobacter spp. was the most misidentified genus (76.9%, 10/13). These results aim to clarify the current biochemical errors in enterobacteria identification, considering isolates from a bovine environment, and show the importance for more careful readings of phenotypic tests which are often used in veterinary microbiology laboratories.

Escherichia coli sequence type 73 as a cause of community acquired urinary tract infection in men and women in Rio de Janeiro, Brazil.

Escherichia coli clones ST131, ST69, ST95, and ST73 are frequent causes of urinary tract infections (UTI) and bloodstream infections. Specific clones and virulence profiles of E. coli causing UTI in men has been rarely described. The aim of this study was to characterize patient and clonal characteristics of community-acquired UTI caused by E. coli in men (n=12) and women (n=127) in Rio de Janeiro, Brazil, complementing a previous work. We characterized isolates in phylogenetic groups, ERIC2-PCR and PFGE types, MLST, genome similarity and virulence gene-profiles. UTI from men were more frequently caused by phylogenetic group B2 isolates (83% versus 42%, respectively, P = 0.01), a group with significantly higher virulence scores compared with women. ST73 was the predominant clone in men (50%) and the second most frequent in women (12%), with the highest virulence score (mean and median=9) among other clones. ST73 gnomes formed at least six clusters. E. coli from men carried significantly higher numbers of virulence genes, such as sfa/focDE (67% versus 27%), hlyA (58% versus 24%), cnf 1 (58% versus 16%), fyuA (100% versus 82%) and MalX (92% versus 44%), compared with isolates from women. These data suggest the predominance and spread of ST73 isolates likely relates to an abundance of virulence determinants.