High prevalence of bla OXA-23 in Acinetobacter spp. and detection of bla NDM-1 in A. soli in Cuba: report from National Surveillance Program (2010-2012)

Phylogenetic Tree 16S rRNA Gene of Acinetobacter soli Isolated from the Prepuce of Aceh Cattle

BACKGROUND: In the pre-seed area of healthy Aceh cattle, it is possible to be contaminated with pathogenic bacteria that can interfere with the reproductive system. This study is needed to identify these pathogenic bacteria using a molecular approach, in an effort to prevent infection. AIM: The aim of the present study was to construct phylogenetic tree relationships of Acinetobacter soli identified in the preputial area of Aceh cattle by molecular analysis using 16S rRNA gene sequencing. MATERIALS AND METHODS: A total of 75 preputial specimens were obtained from Indrapuri’s Breeding and Forages Center of Aceh Cattles, Indrapuri district, Banda Aceh, Indonesia. The samples were processed for culture using standard conventional methods. The extraction of genomic DNA and the amplification of the 16S rRNA gene were assayed using polymerase chain reaction. A phylogenetic tree was constructed using distance matrices using the neighbor-joining model of the molecular evolutionary genetic analysis software 6.1 software. RESULTS: The results showed that of 75 preputial swab samples, 18 (24%) were positive for A. soli isolates. There was a 100% sequence similarity to A. soli prototype strain B1 and a 99% similarity to Acinetobacter parvus prototype strain LUH4616, Acinetobacter baylyi strain B2, A. venetianus strain ATCC 31012, as well as a 99% similarity to Acinetobacter baumannii strain DSM 30007, the strain ATCC 19606, and the strain JCM 6841, respectively. We concluded that A. soli-positive presentation in the preparation of Aceh cattle has 100% sequence similarity of 16S rRNA with A. soli strain B1. CONCLUSIONS: The conclusion of this study is that, based on the construction of a phylogenetic tree, it shows that 24% of the bacterial isolate is related to A. soli. It is essential to conduct a regular survey for bacterial contamination and to increase worker awareness and education about hygiene standards.

Multicenter Study of Carbapenemase-Producing Enterobacterales in Havana, Cuba, 2016–2021

Surveillance of carbapenem resistance is particularly important for Enterobacterales, mainly in countries with limited healthcare resources. We conducted a cross-sectional study to detect carbapenem-resistant Enterobacterales at 10 sentinel hospitals in Havana, Cuba for a six year-period (2016–2021) by the National Reference Laboratory for Health Care-Associated Infections in the Pedro Kourí Institute. A total of 152 isolates were collected with phenotypic production of metallo-β-lactamase. NDM-type carbapenemase was detected in all the 152 isolates, and KPC-type enzyme gene was simultaneously identified in four NDM-positive isolates. The most abundant carbapenemase-producing Enterobacterales (CPE) species was Klebsiella pneumoniae (69.7%), followed by Enterobacter cloacae complex (13.2%), and Escherichia coli (5.9%). Over the study period, among CPE, prevalence of K. pneumoniae was almost constant, while Enterobacter spp. showed slightly increasing tendency. The urinary tract (36.2%) was the most prevalent source of infection with CPE, followed by bloodstream (26.3%) and surgical wound (17.1%), being frequently derived from Intensive Care Units (35.5%) and urology wards (21.7%). This study revealed the present situation of CPE in hospitals in Havana, Cuba, showing the emergence and dissemination of Enterobacterales producing NDM-type carbapenemase, mainly K. pneumoniae.

Withdrawal of Colistin Reduces Incidence of mcr-1-Harboring IncX4-Type Plasmids but Has Limited Effects on Unrelated Antibiotic Resistance

The global dissemination of plasmid-mediated colistin resistance gene mcr and its variants have posed a great threat to public health. Therefore, the Chinese government banned the use of colistin as a feed additive in livestock in April 2017. To explore the dynamic changes of overall antibiotic resistance genes (ARGs) and phylogenetic relationship of bacteria from a single pig farm before and after the withdrawal of colistin, fecal swab samples were collected from a large-scale pig farm before (n = 32; 2 months pre-withdrawal of colistin) and after withdrawal of colistin (n = 30; 13 months post-withdrawal of colistin). Escherichia coli and Klebsiella pneumoniae were isolated. Whole-genome sequencing (Illumina, MiSeq) was performed to examine ARGs, plasmids and the genetic relationship of the isolates. The overall SNP results indicated all isolates had high genetic diversity, and the evolutionary relationship across isolates was not influenced by the ban of colistin. However, the prevalence of mcr-1.1 (5.6%, p < 0.01) was significantly lower than before the ban (86.4%). Plasmid profiling analysis showed that 17 of 20 (85.0%) observed mcr-1.1 genes reside on IncX4-type plasmids, 16 of which (94.1%) were from isolates before the ban. On the contrary, the presence of blaCTX-M gene was significantly increased (p = 0.0215) post-withdrawal of colistin. Our results showed that withdrawal of colistin reduced the incidence of mcr-1-harboring IncX4-type plasmids, but had limited influences on unrelated ARGs.

Mapping Global Prevalence of Acinetobacter baumannii and Recent Vaccine Development to Tackle It

Acinetobacter baumannii is a leading cause of nosocomial infections that severely threaten public health. The formidable adaptability and resistance of this opportunistic pathogen have hampered the development of antimicrobial therapies which consequently leads to very limited treatment options. We mapped the global prevalence of multidrug-resistant A. baumannii and showed that carbapenem-resistant A. baumannii is widespread throughout Asia and the Americas. Moreover, when antimicrobial resistance rates of Acinetobacter spp. exceed a threshold level, the proportion of A. baumannii isolates from clinical samples surges. Therefore, vaccines represent a realistic alternative strategy to tackle this pathogen. Research into anti-A. baumannii vaccines have enhanced in the past decade and multiple antigens have been investigated preclinically with varying results. This review summarises the current knowledge of virulence factors relating to A. baumannii–host interactions and its implication in vaccine design, with a view to understanding the current state of A. baumannii vaccine development and the direction of future efforts.

Characterization of Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Pigs in Cuba Using Next-Generation Sequencing

Resistance to third-generation cephalosporins (3GC) in Escherichia coli has been reported worldwide from humans and animals, but the situation in Cuba is still poorly understood. This study aimed to gain new insights into the phenotypic and genotypic characteristics of third-generation cephalosporin-resistant (3GC-R) E. coli isolated from pigs in Cuba. Rectal swabs from 215 healthy pigs were taken from different municipalities in the western region of Cuba and spread on MacConkey agar supplemented with cefotaxime and ceftazidime. Ninety-six isolates were identified as 3GC-R E. coli and 87.5% of them were resistant to at least three antibiotic classes as determined by the measurement of the minimum inhibitory concentration (MIC) of 14 antibiotics. Twenty-seven different isolates were selected for Illumina next-generation sequencing, and subsequent in silico analysis was performed for the detection of antibiotic resistance and virulence genes, plasmid incompatibility (Inc) groups, multilocus sequence typing (MLST), and core genome MLST (cgMLST). The sequenced isolates contained extended-spectrum β-lactamase genes bla_CTX-M-32 (n = 17), bla_CTX-M-15 (n = 5), and bla_CTX-M-55 (n = 4) as well as with pAmpC gene bla_CMY-2 (n = 2). They also harbored genes for resistance to other clinically important classes of antibiotics, as well as several diverse virulence factors. The 3GC-R E. coli were genetically highly diverse, belonging to 16 different sequence types. IncX1 was the most frequent Inc group. The presence of 3GC-R E. coli in pigs from Cuba containing several different antibiotic resistance mechanisms emphasizes the need for surveillance programs and the establishment of strategies for the prudent use of antibiotics in food-producing animals.

Multidrug-resistant Acinetobacter baumannii outbreaks: a global problem in healthcare settings

INTRODUCTION

The increase in the prevalence of multidrug-resistant Acinetobacter baumannii infections in hospital settings has rapidly emerged worldwide as a serious health problem.

METHODS

This review synthetizes the epidemiology of multidrug-resistant A. baumannii, highlighting resistance mechanisms.

CONCLUSIONS

Understanding the genetic mechanisms of resistance as well as the associated risk factors is critical to develop and implement adequate measures to control and prevent acquisition of nosocomial infections, especially in an intensive care unit setting.

High Prevalence of CTX-M Type Extended-Spectrum Beta-Lactamase Genes and Detection of NDM-1 Carbapenemase Gene in Extraintestinal Pathogenic Escherichia coli in Cuba

Increase of extraintestinal pathogenic Escherichia coli (ExPEC) showing resistance to beta-lactams is a major public health concern. This study was conducted as a first molecular epidemiological study on ExPEC in Cuba, regarding prevalence of extended-spectrum beta-lactamases (ESBLs) and carbapenemase genes. A total of 306 ExPEC isolates collected in medical institutions in 16 regions in Cuba (2014–2018) were analyzed for their genotypes and presence of genes encoding ESBL, carbapenemase, plasmid-mediated quinolone resistance (PMQR) determinants by PCR and sequencing. The most common phylogenetic group of ExPEC was B2 (49%), followed by D (23%), A (21%), and B1 (7%). Among ESBL genes detected, bla_CTX-M was the most common and detected in 61% of ExPEC, with bla_CTX-M-15 being dominant and distributed to all the phylogenetic groups. NDM-1 type carbapenemase gene was identified in two isolates of phylogenetic group B1-ST448. Phylogenetic group B2 ExPEC belonged to mostly ST131 (or its single-locus variant) with O25b allele, harboring bla_CTX-M-27, and included an isolate of emerging type ST1193. aac (6’)-Ib-cr was the most prevalent PMQR gene (40.5%), being present in 54.5% of CTX-M-positive isolates. These results indicated high prevalence of CTX-M genes and the emergence of NDM-1 gene among recent ExPEC in Cuba, depicting an alarming situation.

First Report of New Delhi Metallo-β-Lactamase Carbapenemase-Producing Acinetobacter baumannii in Peru

Here we report the first incidence of New Delhi metallo-β-lactamase (NDM-1)-producing Acinetobacter baumannii in Peru, identified via a strain-based nosocomial surveillance project carried out in Lima and Iquitos. The bla _NDM-1 gene was detected by multiplex polymerase chain reaction (PCR) and confirmed by loci sequencing. Acinetobacter baumannii is a nearly ubiquitous and promiscuous nosocomial pathogen, and the acquisition of bla _NDM-1 by A. baumannii may facilitate an increase in the prevalence of this important resistance marker in other nosocomial pathogens.

What's new in the treatment of multidrug-resistant gram-negative infections?

Eradicating multi-drug resistant (MDR) organisms has been a major challenge in healthcare settings worldwide. Newly approved drugs and those currently in the pipeline may have a promising solution to this issue. The purposes of this review are to describe the various resistance mechanisms of Gram-negative bacteria and to provide a summary of the current literature available on the newer agents, such as ceftazidime/avibactam, ceftolozane/tazobactam, meropenem/vaborbactam, and other emerging agents used for the treatment of MDR Gram-negative infections. Given that MDR organisms confer resistance to treatment by various methods, including enzymatic degradation, efflux pumps, and porin mutation, an understanding of mechanisms of bacterial resistance combined with information on newer antimicrobial agents against MDR Gram-negative bacteria will further assist clinicians in determining the best suitable therapy for the treatment of various complicated infections.

Analysis of beta-lactamases, blaNDM-1phylogeny & plasmid replicons in multidrug-resistant Klebsiella spp. from a tertiary care centre in south India

Background & objectives:

β-lactamases play a predominant role in drug-resistance amongst Enterobacteriaceae. Presence of genes on transferable plasmids encoding these enzymes favours their dissemination across species and genera within and outside geographical boundaries. This study was aimed to understand the presence of β-lactamases and transferable plasmids in clinical isolates of Klebsiella spp. which can contribute to the spread of resistance determinants.

Methods:

A total of 41 clinical isolates of Klebsiella spp., collected from a tertiary care centre in Kerala, India, were checked for antibiotic sensitivity and the presence of plasmids. The ability to produce extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs) was screened for and confirmed in 29 plasmid-harbouring isolates. bla_NDM-1-specific primers were used for polymerase chain reaction amplification with plasmid DNA as template to determine episomal prevalence of this gene and its sequence-based phylogeny employing similar sequences from GenBank. Plasmid replicon typing was also carried out to determine the presence of transferable plasmids.

Results:

Our results showed a high degree of multidrug-resistant (MDR) pathogens with ESBL production confirmed in 52 per cent, MBL in 31 per cent and co-production of both enzymes in seven per cent of the plasmid-bearing isolates. Plasmid DNA from 14 per cent of the isolates produced bla_NDM-1-specific amplicons which showed sequence homology with those from bacteria of different genera and geographical areas. The predominant replicon type was found to be that of conjugative plasmids belonging to the incompatibility group - IncFII_K.

Interpretation & conclusions:

This study provides insight into the predominance of various β-lactamases and potent gene-disseminating agents in Klebsiella spp. and emphasizes the need for constant surveillance of these pathogens to determine appropriate treatment strategies.

Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance

Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene bla_NDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of bla_NDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian doll model for the dissemination of bla_NDM-1 in Latin America, with P. rettgeri playing a central role in this process, and reveal new insights into the evolution and dissemination of plasmids carrying such antibiotic resistance genes.

The role of the genetic elements bla oxa and IS Aba 1 in the Acinetobacter calcoaceticus-Acinetobacter baumannii complex in carbapenem resistance in the hospital setting

INTRODUCTION

Members of the Acinetobacter genus are key pathogens that cause healthcare-associated infections, and they tend to spread and develop new antibiotic resistance mechanisms. Oxacillinases are primarily responsible for resistance to carbapenem antibiotics. Higher rates of carbapenem hydrolysis might be ascribed to insertion sequences, such as the ISAba1 sequence, near bla OXA genes. The present study examined the occurrence of the genetic elements bla OXA and ISAba1 and their relationship with susceptibility to carbapenems in clinical isolates of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex.

METHODS

Isolates identified over 6 consecutive years in a general hospital in Joinville, Southern Brazil, were evaluated. The investigation of 5 families of genes encoding oxacillinases and the ISAba1 sequence location relative to bla OXA genes was conducted using polymerase chain reaction.

RESULTS

All isolates presented the bla OXA-51-like gene (n = 78), and 91% tested positive for the bla OXA-23-like gene (n = 71). The presence of ISAba1 was exclusively detected in isolates carrying the bla OXA-23-like gene. All isolates in which ISAba1 was found upstream of the bla OXA-23-like gene (n = 69) showed resistance to carbapenems, whereas the only isolate in which ISAba1 was not located near the bla OXA-23-like gene was susceptible to carbapenems. The ISAba1 sequence position of another bla OXA-23-like-positive isolate was inconclusive. The isolates exclusively carrying the bla OXA-51-like gene (n = 7) showed susceptibility to carbapenems.

CONCLUSIONS

The presence of the ISAba1 sequence upstream of the bla OXA-23-like gene was strongly associated with carbapenem resistance in isolates of the A. calcoaceticus-A. baumannii complex in the hospital center studied.

IncFII Conjugative Plasmid-Mediated Transmission of blaNDM-1 Elements among Animal-Borne Escherichia coli Strains

This study aims to investigate the prevalence and transmission dynamics of the bla_NDM-1 gene in animal Escherichia coli strains. Two IncFII bla_NDM-1-encoding plasmids with only minor structural variation in the MDR region, pHNEC46-NDM and pHNEC55-NDM, were found to be responsible for the transmission of bla_NDM-1 in these strains. The bla_NDM-1 gene can be incorporated into plasmids and stably inherited in animal-borne E. coli strains that can be maintained in animal gut microflora even without carbapenem selection pressure.

The epidemiology of carbapenemases in Latin America and the Caribbean

INTRODUCTION

Enterobacteriaceae, Pseudomonas spp., and Acinetobacter spp. infections are major causes of morbidity and mortality, especially due to the emergence and spread of β-lactamases. Carbapenemases, which are β-lactamases with the capacity to hydrolyze or inactivate carbapenems, have become a serious concern as they have the largest hydrolytic spectrum and therefore limit the utility of most β-lactam antibiotics. Areas covered: Here, we present an update of the current status of carbapenemases in Latin America and the Caribbean. Expert commentary: The increased frequency of reports on carbapenemases in Latin America and the Caribbean shows that they have successfully spread and have even become endemic in some countries. Countries such as Brazil, Colombia, Argentina, and Mexico account for the majority of these reports. Early suspicion and detection along with implementation of antimicrobial stewardship programs in all healthcare settings are crucial for the control and prevention of carbapenemase-producing bacteria.

Multilocus Sequence Typing Analysis of Carbapenem-Resistant Acinetobacter baumannii in a Chinese Burns Institute

Acinetobacter baumannii is a leading pathogen responsible for nosocomial infections. The emergence of carbapenem-resistant A. baumannii (CRAB) has left few effective antibiotics for clinicians to use. To investigate the temporal evolutionary relationships among CRAB strains, we collected 248 CRAB isolates from a Chinese burns institute over 3 years. The prevalence of the OXA-23 gene was detected by polymerase chain reaction. Multilocus sequence typing was used to type the CRAB strains and eBURST was used to analyze their evolutionary relationships. Wound surfaces (41%), sputa (24%), catheters (15%), and bloods (14%) were the four dominant isolation sources. Except for minocycline (33.5%) and sulbactam/cefoperazone (74.6%), these CRAB strains showed high resistance rates (>90%) to 16 tested antibiotics. The 248 isolates fall into 26 sequence types (STs), including nine known STs and 17 unknown STs. The majority (230/248) of these isolates belong to clonal complex 92 (CC92), including eight isolates belonging to seven unreported STs. A new CC containing 11 isolates grouped into four new STs was identified. The OXA-23 gene was detected at high prevalence among the CRAB isolates and the prevalence rate among the various STs differed. The majority of the isolates displayed a close evolutionary relationship, suggesting that serious nosocomial spreading and nosocomial infections of CRAB have occurred in the burn unit. In conclusion, the main CC for CRAB in this Chinese burn unit remained unchanged during the 3-year study period, and a new CC was identified. CC92 was the dominant complex, and more attention should be directed toward monitoring the new CC we have identified herein.

Reservoirs of Non-baumannii Acinetobacter Species

Acinetobacter spp. are ubiquitous gram negative and non-fermenting coccobacilli that have the ability to occupy several ecological niches including environment, animals and human. Among the different species, Acinetobacter baumannii has evolved as global pathogen causing wide range of infection. Since the implementation of molecular techniques, the habitat and the role of non-baumannii Acinetobacter in human infection have been elucidated. In addition, several new species have been described. In the present review, we summarize the recent data about the natural reservoir of non-baumannii Acinetobacter including the novel species that have been described for the first time from environmental sources and reported during the last years.