Pathogens

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8 pages, 1226 KiB

Open AccessCommunication

Genomic Features of an MDR Escherichia coli ST5506 Harboring an IncHI2/In229/bla_CTX-M-2 Array Isolated from a Migratory Black Skimmer

by Quézia Moura, Miriam R. Fernandes, Fábio P. Sellera, Brenda Cardoso, Cristiane L. Nascimento, Gustavo H. P. Dutra and Nilton Lincopan

Pathogens 2024, 13(1), 63; https://doi.org/10.3390/pathogens13010063 - 09 Jan 2024

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Abstract

Migratory birds have contributed to the dissemination of multidrug-resistant (MDR) bacteria across the continents. A CTX-M-2-producing Escherichia coli was isolated from a black skimmer (Rynchops niger) in Southeast Brazil. The whole genome was sequenced using the Illumina NextSeq platform and de [...] Read more.

Migratory birds have contributed to the dissemination of multidrug-resistant (MDR) bacteria across the continents. A CTX-M-2-producing Escherichia coli was isolated from a black skimmer (Rynchops niger) in Southeast Brazil. The whole genome was sequenced using the Illumina NextSeq platform and de novo assembled by CLC. Bioinformatic analyses were carried out using tools from the Center for Genomic Epidemiology. The genome size was estimated at 4.9 Mb, with 4790 coding sequences. A wide resistome was detected, with genes encoding resistance to several clinically significant antimicrobials, heavy metals, and biocides. The bla_CTX-M-2 gene was inserted in an In229 class 1 integron inside a ∆TnAs3 transposon located in an IncHI2/ST2 plasmid. The strain was assigned to ST5506, CH type fumC19/fimH32, serotype O8:K87, and phylogroup B1. Virulence genes associated with survival in acid conditions, increased serum survival, and adherence were also identified. These data highlight the role of migratory seabirds as reservoirs and carriers of antimicrobial resistance determinants and can help to elucidate the antimicrobial resistance dynamics under a One Health perspective. Full article

(This article belongs to the Special Issue Detection and Epidemiology of Drug-Resistant Bacteria)

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17 pages, 4431 KiB

Open AccessArticle

Clonal Diversity, Antibiotic Resistance, and Virulence Factor Prevalence of Community Associated Staphylococcus aureus in Southeastern Virginia

by Katelyn D. Cranmer, Mohan D. Pant, Suzanne Quesnel and Julia A. Sharp

Pathogens 2024, 13(1), 25; https://doi.org/10.3390/pathogens13010025 - 27 Dec 2023

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Abstract

Staphylococcus aureus is a significant human pathogen with a formidable propensity for antibiotic resistance. Worldwide, it is the leading cause of skin and soft tissue infections (SSTI), septic arthritis, osteomyelitis, and infective endocarditis originating from both community- and healthcare-associated settings. Although often grouped [...] Read more.

Staphylococcus aureus is a significant human pathogen with a formidable propensity for antibiotic resistance. Worldwide, it is the leading cause of skin and soft tissue infections (SSTI), septic arthritis, osteomyelitis, and infective endocarditis originating from both community- and healthcare-associated settings. Although often grouped by methicillin resistance, both methicillin-resistant (MRSA) and methicillin-sensitive (MSSA) strains are known to cause significant pathologies and injuries. Virulence factors and growing resistance to antibiotics play major roles in the pathogenicity of community-associated strains. In our study, we examined the genetic variability and acquired antibiograms of 122 S. aureus clinical isolates from SSTI, blood, and urinary tract infections originating from pediatric patients within the southeast region of Virginia, USA. We identified a suite of clinically relevant virulence factors and evaluated their prevalence within these isolates. Five genes (clfA, spA, sbi, scpA, and vwb) with immune-evasive functions were identified in all isolates. MRSA isolates had a greater propensity to be resistant to more antibiotics as well as significantly more likely to carry several virulence factors compared to MSSA strains. Further, the carriage of various genes was found to vary significantly based on the infection type (SSTI, blood, urine). Full article

(This article belongs to the Special Issue Detection and Epidemiology of Drug-Resistant Bacteria)

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11 pages, 4903 KiB

Open AccessCommunication

Genomic Insights into Pluralibacter gergoviae Sheds Light on Emergence of a Multidrug-Resistant Species Circulating between Clinical and Environmental Settings

by João Pedro Rueda Furlan and Eliana Guedes Stehling

Pathogens 2023, 12(11), 1335; https://doi.org/10.3390/pathogens12111335 - 09 Nov 2023

Cited by 1 | Viewed by 1244

Abstract

Pluralibacter gergoviae is a member of the Enterobacteriaceae family that has been reported sporadically. Although P. gergoviae strains exhibiting multidrug-resistant profiles have been identified an in-depth genomic analysis focusing on antimicrobial resistance (AMR) has been lacking, and was therefore performed in this study. [...] Read more.

Pluralibacter gergoviae is a member of the Enterobacteriaceae family that has been reported sporadically. Although P. gergoviae strains exhibiting multidrug-resistant profiles have been identified an in-depth genomic analysis focusing on antimicrobial resistance (AMR) has been lacking, and was therefore performed in this study. Forty-eight P. gergoviae strains, isolated from humans, animals, foods, and the environment during 1970–2023, were analyzed. A large number of single-nucleotide polymorphisms were found, indicating a highly diverse population. Whilst P. gergoviae strains were found to be circulating at the One Health interface, only human and environmental strains exhibited multidrug resistance genotypes. Sixty-one different antimicrobial resistance genes (ARGs) were identified, highlighting genes encoding mobile colistin resistance, carbapenemases, and extended-spectrum β-lactamases. Worryingly, the co-occurrence of mcr-9.1, bla_KPC-2, bla_CTX-M-9, and bla_SHV-12, as well as mcr-10.1, bla_NDM-5, and bla_SHV-7, was detected. Plasmid sequences were identified as carrying clinically important ARGs, evidencing IncX3 plasmids harboring bla_KPC-2, bla_NDM-5, or bla_SHV-12 genes. Virulence genotyping underlined P. gergoviae as being a low-virulence species. In this regard, P. gergoviae is emerging as a new multidrug-resistant species belonging to the Enterobacteriaceae family. Therefore, continuous epidemiological genomic surveillance of P. gergoviae is required. Full article

(This article belongs to the Special Issue Detection and Epidemiology of Drug-Resistant Bacteria)

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12 pages, 1900 KiB

Open AccessEditor’s ChoiceArticle

Epidemiological Characteristics of Carbapenem-Resistant Enterobacterales in Japan: A Nationwide Analysis of Data from a Clinical Laboratory Center (2016–2022)

by Kentarou Takei, Miho Ogawa, Ryuji Sakata and Hajime Kanamori

Pathogens 2023, 12(10), 1246; https://doi.org/10.3390/pathogens12101246 - 16 Oct 2023

Cited by 1 | Viewed by 1316

Abstract

In Japan, nationwide epidemiological surveys on carbapenem-resistant Enterobacterales (CREs), including comprehensive information, are scarce, with most data available only through public reports. This study analyzed data on the Enterobacterales family collected from nationwide testing centers between January 2016 and December 2022, focusing on [...] Read more.

In Japan, nationwide epidemiological surveys on carbapenem-resistant Enterobacterales (CREs), including comprehensive information, are scarce, with most data available only through public reports. This study analyzed data on the Enterobacterales family collected from nationwide testing centers between January 2016 and December 2022, focusing on isolates that met the criteria for CRE in Japan based on drug susceptibility. We investigated 5,323,875 Enterobacterales isolates of 12 different species; among 4696 (0.09%) CRE strains, the proportion of major CRE isolates was as follows: Escherichia coli, 31.3%; Klebsiella pneumoniae, 28.0%; Enterobacter cloacae, 18.5%; and Klebsiella aerogenes, 6.7%. Moreover, over a 7-year period, Providencia rettgeri, E. cloacae, K. aerogenes, and K. pneumoniae demonstrated relatively high CRE percentages of 0.6% (156/26,185), 0.47% (869/184,221), 0.28% (313/110,371), and 0.17% (1314/780,958), respectively. The number of CRE strains isolated from different samples was as follows: urine, 2390; respiratory specimens, 1254; stool, 425; blood, 252; others, 375. In the broader context, including colonization, the predominant isolates of CREs collected at nationwide testing centers are E. coli and K. pneumoniae. Furthermore, recently, attention has been directed toward less common CRE species, such as Klebsiella oxytoca and Providencia rettgeri, and thus, it might be necessary to continue monitoring these less common species. Full article

(This article belongs to the Special Issue Detection and Epidemiology of Drug-Resistant Bacteria)

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7 pages, 1435 KiB

Open AccessCommunication

One Health Spread of 16S Ribosomal RNA Methyltransferase-Harboring Gram-Negative Bacterial Genomes: An Overview of the Americas

by Fábio Parra Sellera, Danny Fuentes-Castillo and João Pedro Rueda Furlan

Pathogens 2023, 12(9), 1164; https://doi.org/10.3390/pathogens12091164 - 15 Sep 2023

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Abstract

Aminoglycoside antimicrobials remain valuable therapeutic options, but their effectiveness has been threatened by the production of bacterial 16S ribosomal RNA methyltransferases (16S-RMTases). In this study, we evaluated the genomic epidemiology of 16S-RMTase genes among Gram-negative bacteria circulating in the American continent. A total [...] Read more.

Aminoglycoside antimicrobials remain valuable therapeutic options, but their effectiveness has been threatened by the production of bacterial 16S ribosomal RNA methyltransferases (16S-RMTases). In this study, we evaluated the genomic epidemiology of 16S-RMTase genes among Gram-negative bacteria circulating in the American continent. A total of 4877 16S-RMTase sequences were identified mainly in Enterobacterales and nonfermenting Gram-negative bacilli isolated from humans, animals, foods, and the environment during 1931–2023. Most of the sequences identified were found in the United States, Brazil, Canada, and Mexico, and the prevalence of 16S-RMTase genes have increased in the last five years (2018–2022). The three species most frequently carrying 16S-RMTase genes were Acinetobacter baummannii, Klebsiella pneumoniae, and Escherichia coli. The armA gene was the most prevalent, but other 16S-RMTase genes (e.g., rmtB, rmtE, and rmtF) could be emerging backstage. More than 90% of 16S-RMTase sequences in the Americas were found in North American countries, and although the 16S-RMTase genes were less prevalent in Central and South American countries, these findings may be underestimations due to limited genomic data. Therefore, whole-genome sequence-based studies focusing on aminoglycoside resistance using a One Health approach in low- and middle-income countries should be encouraged. Full article

(This article belongs to the Special Issue Detection and Epidemiology of Drug-Resistant Bacteria)

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12 pages, 1057 KiB

Open AccessCommunication

Antimicrobial Resistance and Extended-Spectrum Beta-Lactamase Genes in Enterobacterales, Pseudomonas and Acinetobacter Isolates from the Uterus of Healthy Mares

by Pamela Thomson, Patricia García, Camila del Río, Rodrigo Castro, Andrea Núñez and Carolina Miranda

Pathogens 2023, 12(9), 1145; https://doi.org/10.3390/pathogens12091145 - 08 Sep 2023

Cited by 1 | Viewed by 1339

Abstract

Antibiotic-resistant bacteria are a growing concern for human and animal health. The objective of this study was to determine the antimicrobial resistance and extended-spectrum beta-lactamase genes in Enterobacterales, Pseudomonas spp. and Acinetobacter spp. isolates from the uterus of healthy mares. For this [...] Read more.

Antibiotic-resistant bacteria are a growing concern for human and animal health. The objective of this study was to determine the antimicrobial resistance and extended-spectrum beta-lactamase genes in Enterobacterales, Pseudomonas spp. and Acinetobacter spp. isolates from the uterus of healthy mares. For this purpose, 21 mares were swabbed for samples, which were later seeded on blood agar and MacConkey agar. The isolates were identified using MALDI-TOF and the antimicrobial susceptibility test was performed using the Kirby–Bauer technique. To characterize the resistance genes, a polymerase chain reaction (PCR) scheme was performed. Of the isolates identified as Gram-negative, 68.8% were Enterobacterales, represented by E. coli, Enterobacter cloacae, Citrobacter spp., and Klebsiella pneumoniae; 28.1% belonged to the genus Acinetobacter spp.; and 3.1% to Pseudomonas aeruginosa. A 9.3% of the isolates were multidrug-resistant (MDR), presenting resistance to antibiotics from three different classes, while 18.8% presented resistance to two or more classes of different antibiotics. The diversity of three genes that code for ESBL (bla_TEM, bla_CTX-M and bla_SHV) was detected in 12.5% of the strains. The most frequent was bla_SHV, while bla_TEM and bla_CTX-M were present in Citrobacter spp. and Klebsiella pneumoniae. These results are an alarm call for veterinarians and their environment and suggest taking measures to prevent the spread of these microorganisms. Full article

(This article belongs to the Special Issue Detection and Epidemiology of Drug-Resistant Bacteria)

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14 pages, 1372 KiB

Open AccessArticle

Clinically Isolated β-Lactam-Resistant Gram-Negative Bacilli in a Philippine Tertiary Care Hospital Harbor Multi-Class β-Lactamase Genes

by Alecks Megxel S. Abordo, Mark B. Carascal, Roland Remenyi, Doralyn S. Dalisay and Jonel P. Saludes

Pathogens 2023, 12(8), 1019; https://doi.org/10.3390/pathogens12081019 - 08 Aug 2023

Viewed by 1999

Abstract

In the Philippines, data are scarce on the co-occurrence of multiple β-lactamases (BLs) in clinically isolated Gram-negative bacilli. To investigate this phenomenon, we characterized BLs from various β-lactam-resistant Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa isolated from a [...] Read more.

In the Philippines, data are scarce on the co-occurrence of multiple β-lactamases (BLs) in clinically isolated Gram-negative bacilli. To investigate this phenomenon, we characterized BLs from various β-lactam-resistant Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa isolated from a Philippine tertiary care hospital. The selected Gram-negative bacilli (n = 29) were resistant to either third-generation cephalosporins (resistance category 1 (RC1)), cephalosporins and penicillin-β-lactamase inhibitors (RC2), or carbapenems (RC3). Isolates resistant to other classes of antibiotics but susceptible to early-generation β-lactams were also selected (RC4). All isolates underwent antibiotic susceptibility testing, disk-diffusion-based BL detection assays, and PCR with sequence analysis of extended-spectrum BLs (ESBLs), metallo-BLs, AmpC BLs, and oxacillinases. Among the study isolates, 26/29 harbored multi-class BLs. All RC1 isolates produced ESBLs, with bla_CTX-M as the dominant (19/29) gene. RC2 isolates produced ESBLs, four of which harbored bla_TEM plus bla_OXA-1 or other ESBL genes. RC3 isolates carried bla_NDM and bla_IMP_, particularly in three of the metallo-BL producers. RC4 Enterobacteriaceae carried bla_CTX-M, bla_TEM, and bla_OXA-24-like, while A. baumannii and P. aeruginosa in this category carried either bla_IMP or bla_OXA-24. Genotypic profiling, in complement with phenotypic characterization, revealed multi-class BLs and cryptic metallo-BLs among β-lactam-resistant Gram-negative bacilli. Full article

(This article belongs to the Special Issue Detection and Epidemiology of Drug-Resistant Bacteria)

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11 pages, 901 KiB

Open AccessArticle

Genomics and Antimicrobial Susceptibility of Clinical Pseudomonas aeruginosa Isolates from Hospitals in Brazil

by Carlos Henrique Camargo, Amanda Yaeko Yamada, Andreia Rodrigues de Souza, Marisa de Jesus de Castro Lima, Marcos Paulo Vieira Cunha, Pedro Smith Pereira Ferraro, Claudio Tavares Sacchi, Marlon Benedito Nascimento dos Santos, Karoline Rodrigues Campos, Monique Ribeiro Tiba-Casas, Maristela Pinheiro Freire and Pasqual Barretti

Pathogens 2023, 12(7), 918; https://doi.org/10.3390/pathogens12070918 - 08 Jul 2023

Cited by 1 | Viewed by 1142

Abstract

Pseudomonas aeruginosa, an opportunistic pathogen causing infections in immunocompromised patients, usually shows pronounced antimicrobial resistance. In recent years, the frequency of carbapenemases in P. aeruginosa has decreased, which allows use of new beta-lactams/combinations in antimicrobial therapy. Therefore, the in vitro evaluation of [...] Read more.

Pseudomonas aeruginosa, an opportunistic pathogen causing infections in immunocompromised patients, usually shows pronounced antimicrobial resistance. In recent years, the frequency of carbapenemases in P. aeruginosa has decreased, which allows use of new beta-lactams/combinations in antimicrobial therapy. Therefore, the in vitro evaluation of these drugs in contemporary isolates is warranted. We evaluated the antimicrobial susceptibility and genomic aspects of 119 clinical P. aeruginosa isolates from 24 different hospitals in Brazil in 2021–2022. Identification was performed via MALDI-TOF-MS, and antimicrobial susceptibility was identified through broth microdilution, gradient tests, or disk diffusion. Whole-genome sequencing was carried out using NextSeq equipment. The most active drug was cefiderocol (100%), followed by ceftazidime–avibactam (94.1%), ceftolozane–tazobactam (92.4%), and imipenem–relebactam (81.5%). Imipenem susceptibility was detected in 59 isolates (49.6%), and the most active aminoglycoside was tobramycin, to which 99 (83.2%) isolates were susceptible. Seventy-one different sequence types (STs) were detected, including twelve new STs described herein. The acquired resistance genes bla_CTX-M-2 and bla_KPC-2 were identified in ten (8.4%) and two (1.7%) isolates, respectively. Several virulence genes (exoSTUY, toxA, aprA, lasA/B, plcH) were also identified. We found that new antimicrobials are effective against the diverse P. aeruginosa population that has been circulating in Brazilian hospitals in recent years. Full article

(This article belongs to the Special Issue Detection and Epidemiology of Drug-Resistant Bacteria)

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