Low prevalence of resistance genes in sheltered homeless population in Marseille, France, 2014-2018

Correction: Distinguishing Body Lice from Head Lice by Multiplex Real-Time PCR Analysis of the Phum_PHUM540560 Gene

[This corrects the article DOI: 10.1371/journal.pone.0058088.].

Extended-Spectrum β-Lactamases (ESBL) Producing Bacteria in Animals

Animals have been identified as potential reservoirs and vectors of resistance genes, with studies showing that Gram-negative bacteria can acquire resistance through the horizontal transmission of resistance genes on plasmids. It is important to understand the distribution of antimicrobial-resistant bacteria and their drug-resistant genes in animals. Previous review articles mostly focused on a single bacterium or a single animal. Our objective is to compile all ESBL-producing bacteria isolated from various animals in recent years and provide a comprehensive viewpoint. Using a thorough PubMed literature search spanning from 1 January 2020 to 30 June 2022, studies exploring extended-spectrum beta-lactamase (ESBL) producing bacteria in animals were included. ESBL-producing bacteria are present in animals from various countries around the world. The most common sources of these bacteria were farm animals, and the most frequently isolated bacteria were Escherichia coli and Klebsiella pneumoniae. The most detected ESBL genes were blaTEM, blaSHV, and blaCTX-M. The presence of ESBL-producing bacteria in animals highlights the importance of the One Health approach to address the issue of antibiotic resistance. Further research is needed to better understand the epidemiology and mechanisms of the spread of ESBL-producing bacteria in animal populations and their potential impact on human and animal health.

Urban monitoring of antimicrobial resistance during a COVID-19 surge through wastewater surveillance

During the early phase of the COVID-19 pandemic, infected patients presented with symptoms similar to bacterial pneumonias and were treated with antibiotics before confirmation of a bacterial or fungal co-infection. We reasoned that wastewater surveillance could reveal potential relationships between reduced antimicrobial stewardship, specifically misprescribing antibiotics to treat viral infections, and the occurrence of antimicrobial resistance (AMR) in an urban community. Here, we analyzed microbial communities and AMR profiles in sewage samples from a wastewater treatment plant (WWTP) and a community shelter in Las Vegas, Nevada during a COVID-19 surge in December 2020. Using a respiratory pathogen and AMR enrichment next-generation sequencing panel, we identified four major phyla in the wastewater, including Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria. Consistent with antibiotics that were reportedly used to treat COVID-19 infections (e.g., fluoroquinolones and beta-lactams), we also measured a significant spike in corresponding AMR genes in the wastewater samples. AMR genes associated with colistin resistance (mcr genes) were also identified exclusively at the WWTP, suggesting that multidrug resistant bacterial infections were being treated during this time. We next compared the Las Vegas sewage data to local 2018-2019 antibiograms, which are antimicrobial susceptibility profile reports about common clinical pathogens. Similar to the discovery of higher levels of beta-lactamase resistance genes in sewage during 2020, beta-lactam antibiotics accounted for 51 ± 3 % of reported antibiotics used in antimicrobial susceptibility tests of 2018-2019 clinical isolates. Our data highlight how wastewater-based epidemiology (WBE) can be leveraged to complement more traditional surveillance efforts by providing community-level data to help identify current and emerging AMR threats.

Occurrence of Extended Spectrum Cephalosporin-, Carbapenem- and Colistin-Resistant Gram-Negative Bacteria in Fresh Vegetables, an Increasing Human Health Concern in Algeria

The aim of this study was to screen for extended spectrum cephalosporin-, carbapenem- and colistin-resistant Gram-negative bacteria in fresh vegetables in Batna, Algeria. A total of 400 samples of fresh vegetables were collected from different retail stores. Samples were immediately subjected to selective isolation, then the representative colonies were identified using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF–MS). Phenotypic and genotypic analyses were carried out in terms of species identification and relative antibiotic resistance. Transferability of the carbapenemase and mcr-bearing plasmids was verified by conjugation. The clonal relationships of carbapenemase and mcr-positive Escherichia coli isolates were studied by multi-locus sequence typing (MLST). Sixty-seven isolates were characterised and were mostly isolated from green leafy vegetables, where the dominant species identified included Citrobacter freundii, Klebsiella pneumoniae, Enterobacter cloacae, Stenotrophomona maltophilia, E. coli and Citrobacter braakii. PCR and sequencing results showed that E. coli was the bacterial species presenting the highest antibiotic resistance level in parallel to bla_TEM (n = 16) and bla_CTX-M-15 (n = 11), which were the most detected genes. Moreover, five isolates carried carbapenemase genes, including the bla_OXA-48 and/or bla_VIM-4 genes. The mcr-1 gene was detected in two E. coli isolates. MLST analysis revealed three different E. coli sequence types: ST101 (n = 1), ST216 (n = 1) and ST2298 (n = 1). Conjugation assays confirmed the transferability of the bla_OXA-48 and mcr-1 genes. In this study we report, for the first time, the detection of the bla_OXA-48 gene in E. coli and C. braakii isolates and the bla_VIM-4 gene in vegetables. To the best of our knowledge, this is the first report on the detection of mcr-1 genes from vegetables in Algeria.

Detection of blaOXA-48 and mcr-1 Genes in Escherichia coli Isolates from Pigeon (Columba livia) in Algeria

The emergence and spread of β-lactams and colistin-resistant Escherichia coli in birds deserve a special concern worldwide. This study aimed to investigate the presence of β-lactams and colistin-resistant Escherichia coli strains isolated from the faeces of urban and rural pigeons in Batna, Algeria, and to characterise their molecular traits of resistance. Between March and April 2019, a total of 276 faecal droppings samples were collected in Batna, Algeria. Samples were subjected to selective isolation of β-lactams and colistin-resistant Escherichia coli. The representative colonies were then identified using Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry. Antimicrobial susceptibility testing was performed using the disc diffusion method. β-lactamases, as well as mcr genes, were screened for by PCR and confirmed by sequencing. Genetic relatedness of the mcr-positive E. coli strains was determined using multi-locus sequence typing analysis. Transferability features of carbapenemase genes were assessed by conjugation experiments. Overall, thirty-five E. coli isolates were obtained only from urban pigeon samples. All carbapenem-resistant isolates harboured the bla_OXA-48 gene as the only carbapenemase gene detected (n = 11), while bla_ESBL genes were detected in eighteen isolates. Out of the thirty-five isolates, four E. coli isolates were positive for the mcr-1 gene. The obtained mcr-1 positive E. coli isolates belonged to four STs, including ST1485, ST224, ST46, and a new ST. This study is the first to report the isolation of E. coli strains carrying the mcr-1 gene from pigeon faeces in Algeria and also the first to report the detection of bla_OXA-48-positive E. coli in pigeons. Close surveillance is, therefore, urgently needed to monitor the dissemination of bla_OXA-48 and mcr-1 producing E. coli strains in wildlife.

Detection of NDM-5 and MCR-1 antibiotic resistance encoding genes in Enterobacterales in long-distance migratory bird species Ciconia ciconia, Algeria

β-lactams and colistin resistance in Enterobacterales is a global public health issue. In this study we aimed to investigate the occurrence and genetic determinants of Extended-Spectrum β-lactamases, carbapenemases and mcr-encoding-genes in Enterobacterales isolates recovered from the migratory bird species Ciconia ciconia in an Algerian city. A total of 62 faecal samples from white storks were collected. Samples were then subjected to selective isolation of β-lactams and colistin-resistant-Enterobacterales. The representative colonies were identified using Matrix-Assisted Laser Desorption-Ionisation Time-of-Flight Mass Spectrometry. Susceptibility testing was performed using the disk-diffusion method. ESBL, carbapenemases, and colistin resistance determinants were searched for by PCR and sequencing. The clonality relationships of the obtained isolates were investigated by multilocus sequence typing assays. Mating experiments were carried out to evaluate the transferability of the carbapenemase and mcr-genes. Forty-two isolates were identified as follows: Escherichia coli (n = 33), Klebsiella pneumoniae (n = 4), Proteus mirabilis (n = 4) and Citrobacter freundii (n = 1). Molecular analysis showed that twelve isolates carried the bla_ESBL genes alone, fifteen E. coli isolates were positive for the bla_OXA-48 gene, six isolates were NDM-5-carriers (two P. mirabilis, two K. pneumoniae and two E. coli) and eight E. coli strains were positive for the mcr-1 gene. MLST results showed a high clonal diversity, where NDM-5-producing strains were assigned to two sequence types (ST167 for E. coli and ST198 for K. pneumoniae), whereas the mcr-1 positive E. coli isolates belonged to ST58, ST224, ST453, ST1286, ST2973, ST5542, ST9815 and the international high-risk resistant lineage ST101. To the best of our knowledge, this is the first report of bla_NDM-5 gene in white storks and also the first describing the mcr-1 gene in white storks in Algeria. This study underlines the important role of migratory white storks as carriers of high-level drug-resistant bacteria, allowing their possible implication as indicators and sentinels for antimicrobial resistance surveillance.

First Isolation and Clinical Case of Brevundimonas diminuta in a Newborn with Low Birth Weight, in Democratic Republic of Congo: A Case Report

Brevundimonas diminuta is rarely described in clinical specimens, never at the umbilical stump. Most of the reported cases are in patients with underlying pathologies. We must integrate this microorganism in the etiological agents of nosocomial infections, but much remains to be understood about its virulence. We present a case of umbilical stump infection (omphalitis) caused by B. diminuta, in a preterm and hypotrophic new-born and discuss the diagnosis of this bacterium and its role as responsible of nosocomial neonatal infections.

Epidemiological Investigations of Infectious Diseases among Mobile Populations at the University Hospital Institute Mediterranean Infection in Marseille, France

We review the most recent work conducted by our group on the circulation of infectious agents in mobile populations, including pilgrims participating in the Hajj (Mecca, Saudi Arabia) and the Grand Magal of Touba (Senegal) pilgrimages, homeless people, and medical students participating in an elective abroad. Using a similar epidemiological study design with standardized questionnaires and molecular assays allows comparison of different populations of travelers. The main infectious pathogens and antibiotic resistance genes linked to travel were identified in certain specific populations of travelers, as well as in a group of homeless migrant people in Marseille. The role of several risk factors has also been demonstrated, allowing identifying individuals at increased risk of disease or pathogen carriage on which to base targeted preventive measures. Such results, together with those obtained through international surveillance networks allow better description of the epidemiology of travel-associated infectious diseases.

Enteric pathogenic bacteria and resistance gene carriage in the homeless population in Marseille, France

We aimed to assess the prevalence of pathogenic bacteria and resistance genes in rectal samples collected among homeless persons in Marseille, France. In February 2014 we enrolled 114 sheltered homeless adults who completed questionnaires and had rectal samples collected. Eight types of enteric bacteria and 15 antibiotic resistance genes (ARGs) were sought by real-time polymerase chain reaction (qPCR) performed directly on rectal samples. ARG-positive samples were further tested by conventional PCR and sequencing. We evidenced a 17.5% prevalence of gastrointestinal symptoms, a 9.6% prevalence of enteric pathogenic bacteria carriage, including Escherichia coli pathotypes (8.7%) and Tropheryma whipplei (0.9%). Only 2 persons carried blaCTX-M-15 resistance genes (1.8%), while other genes, including carbapenemase-encoding genes and colistin-resistance genes, (mcr-1 to mcr-6, mcr-8) were not detected. Our results suggest that sheltered homeless persons in Marseille do not have a high risk of harbouring gastrointestinal antibiotic resistant bacteria.

Endemicity of OXA-23 and OXA-72 in clinical isolates of Acinetobacter baumannii from three neighbouring countries in Southeast Europe

According to the World Health Organization, bacterium Acinetobacter baumannii is the first on the critical priority list of pathogens in urgent need for new antibiotics. The increasing resistance of A. baumannii to the last-line treatment options, including carbapenems, is a global problem. We report the molecular epidemiology of 12 carbapenem-resistant clinical isolates of A. baumannii collected from hospitalised patients in three neighbouring countries in Southeast Europe: Croatia, Serbia, and Bosnia and Herzegovina, giving an insight into the molecular characterisation and evolutionary history of the acquisition of resistance genes. Besides the blaOXA-23 gene, the endemic presence of OXA-72 oxacillinase of the same origin for more than a decade as the leading mechanism of carbapenem resistance in Southeast Europe was confirmed. To the best of our knowledge, this is the first paper that investigates and analyses the phylogenetic association of the most common mechanisms of resistance to carbapenems in clinical isolates of A. baumannii originating from three neighbouring countries in Southeast Europe.

Investigation of urban birds as source of β-lactamase-producing Gram-negative bacteria in Marseille city, France

Background

We investigate here the presence of multidrug-resistant bacteria isolated from stool samples of yellow-legged gulls and chickens (n = 136) in urban parks and beaches of Marseille, France. Bacterial isolation was performed on selective media, including MacConkey agar with ceftriaxone and LBJMR medium. Antibiotic resistance genes, including extended-spectrum β-lactamases (ESBL) (i.e. bla_CTX-M, bla_TEM and bla_SHV), carbapenemases (bla_KPC, bla_VIM, bla_NDM, bla_OXA-23, bla_OXA-24, bla_OXA-48 and bla_OXA-58) and colistin resistance genes (mcr-1 to mcr-5) were screened by real-time PCR and standard PCR and sequenced when found.

Results

Of the 136 stools samples collected, seven ESBL-producing Gram-negative bacteria (BGN) and 12 colistin-resistant Enterobacteriaceae were isolated. Among them, five ESBL-producing Escherichia coli and eight colistin-resistant Hafnia alvei strains were identified. Four bla_TEM-1 genes were detected in yellow-legged gulls and chickens. Three CTX-M-15 genes were detected in yellow-legged gulls and pigeons, and one CTX-M-1 in a yellow-legged gull. No mcr-1 to mcr-5 gene were detected in colistin-resistant isolates. Genotyping of E. coli strains revealed four different sequence types already described in humans and animals and one new sequence type.

Conclusions

Urban birds, which are believed to have no contact with antibiotics appear as potential source of ESBL genes. Our findings highlight the important role of urban birds in the proliferation of multidrug-resistant bacteria and also the possible zoonotic transmission of such bacteria from wild birds to humans.