Molecular mechanisms and clonal lineages of colistin-resistant bacteria across the African continent: A scoping review

Colistin (also known as Polymyxin E), a polymyxin antibiotic discovered in the late 1940s, has recently reemerged as a last-line treatment option for multidrug-resistant infections. However, in recent years, colistin-resistant pathogenic bacteria have been increasingly reported worldwide. Accordingly, the presented review was undertaken to identify, integrate and synthesize current information regarding the detection and transmission of colistin-resistant bacteria across the African continent, in addition to elucidating their molecular mechanisms of resistance. PubMed, Google Scholar, and Science Direct were employed for study identification, screening and extraction. Overall, based on the developed literature review protocol and associated inclusion/exclusion criteria, 80 studies published between 2000 and 2021 were included comprising varying bacterial species and hosts. Numerous mechanisms of colistin resistance were reported, including chromosomal mutation(s) and transferable plasmid-mediated colistin resistance (encoded by mcr genes). Perhaps unexpectedly, mcr-variants have exhibited rapid emergence and spread across most African regions. The genetic variant mcr-1 is predominant in humans, animals, and the natural environment, and is primarily carried by IncHI2- type plasmid. The highest numbers of studies reporting the dissemination of colistin-resistant Gram-negative bacteria were conducted in the North African region.

High occurrence of carbapenem-resistant Escherichia coli isolates from healthy rabbits (Oryctolagus cuniculus): first report of blaIMI and blaVIM type genes from livestock in Tunisia

We aimed to study the antibiotic susceptibility and possible occurrence of extended-spectrum beta-lactamases (ESBL)/carbapenemase-producing Escherichia coli isolates collected from rabbits in Tunisia. In all, 35 faecal samples from healthy rabbits were collected from one farm and E. coli were isolated from three media: antibiotic-free TBX agar, TBX+2 mg l^-1 cefotaxime and TBX+1 mg l^-1 imipenem. In total, 39 E. coli isolates were recovered; the majority showed resistance to at least one antibiotic and none was ESBL producer. Carbapenem resistance was detected in 16 isolates from either selective or un-selective media. Phenotypic methods used to detect carbapenemase production showed two positive isolates by Modified Hodge Test, six metallo-carbapenemase producers (Imipenem disc+EDTA) and all were temocillin resistant (possible OXA-48 carbapenemase). bla_VIM and bla_IMP type genes were detected in two and one isolates, respectively; one of them harboured both genes. Isolates contained common genes encoding resistance to sulphonamides (sul1, sul2), tetracycline (tetA, tetB, tetC) and fluoroquinolones (qnrS, aac(6')-Ib-cr). Class 1 and 2 integrons were detected in five and four isolates, respectively. These findings highlight the importance of rabbit production as reservoir of carbapenem-resistant E. coli and argument the first report of bla_VIM and bla_IMP genes in livestock in Tunisia.

Characterization of bacteriocinogenic Enterococcus isolates from wild and laboratory rabbits for the selection of autochthonous probiotic strains in Tunisia

AIM

The objective of this study was to characterize lactic acid bacteria (LAB) from rabbits to be used as potential autochthonous probiotic.

METHODS AND RESULTS

Fifteen faecal samples were collected from wild and laboratory rabbits. One hundred and eight isolates were collected and tested for their inhibitory power against eight pathogenic bacteria. Among them, 43 Enterococcus isolates were able to inhibit at least one pathogen. Enterocine genes entA, entB and entP were detected in 14, 17 and 22 isolates, respectively. These isolates were tested for their antibiotic susceptibility and genes encoding virulence factors. Relevant phenotypes of antibiotic resistance were observed especially for ampicillin, vancomycin and linezolid. The following virulence genes were detected (number of positive isolates): hyl (5), esp (8), gelE (30), agg (2), ace (21), efa (6), CylL_L/s (5), cob (26), cpd (32) and ccf (33). Five isolates were considered as safe and showed tolerance to both acid and bile salt.

CONCLUSION

Bacteriocinogenic enterococci isolates from rabbits may show relevant resistance phenotypes and virulence factors. In addition, one Enterococcus durans isolate presents promising autochthonous probiotic candidate.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study reveals interesting properties for E. durans isolate and supports their utilization as autochthonous probiotic in rabbit husbandry.

Quinolone resistance among Salmonella Kentucky and Typhimurium isolates in Tunisia: first report of Salmonella Typhimurium ST34 in Africa and qnrB19 in Tunisia

AIMS

Characterization of quinolone-resistant Salmonella Kentucky and Typhimurium isolates in Tunisia from various sources, detection of some plasmid-mediated quinolone resistance genes and the genetic relatedness.

METHODS

A total of 1404 isolates of S. Kentucky (n = 1059)/S. Typhimurium (n = 345) from various sources from all over Tunisia were tested for quinolone resistance by disk diffusion method. Minimum inhibitory concentrations of nalidixic acid, ciprofloxacin and ofloxacin were determined. Quinolone-resistant isolates were screened for plasmid-mediated quinolone-resistance genes (qnrA,qnrB,qnrS, aac(6')-Ib-cr and qepA) by polymerase chain reaction (PCR). Mutations in the quinolone-resistance-determining regions of the gyrA and parC genes were detected by PCR and DNA sequencing. Pulsed-field gel electrophoresis and multilocus sequence typing were accomplished for isolates harbouring plasmid-mediated quinolone-resistance genes.

RESULTS

According to our selection criteria (NAL = resistance phenotype; CIP = resistant with diameter 0, or intermediate), only 63 S. Kentucky/41 S. Typhimurium isolates were investigated: 49% (5/104) were multidrug resistant. Two S. Typhimurium isolates harboured qnrB19 with different PFGE profiles. A mutation was detected in the gyrA gene for each of these two isolates. MLST revealed the presence of ST313 and ST34, an endemic sequence type.

CONCLUSION

Our study highlights the presence of quinolone multidrug-resistant Salmonella in humans and animals in Tunisia. This is the first report of S. Typhimurium ST34 in Africa and qnrB19 in Tunisia.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report that describes not only the current epidemiological situation of the quinolone resistance in S. Kentucky and Typhimurium isolated from various sources and regions in Tunisia, but also, the genetic resistance determinants associated with phenotypic antibiotic resistance and the molecular mechanisms of their quinolone-resistance. Also, we provide the first report of S. Typhimurium ST34 in Africa, and the first report of qnrB19 in Salmonella in Tunisia.

High occurrence of enterotoxigenic isolates and low antibiotic resistance rates of Staphylococcus aureus isolated from raw milk from cows and ewes

This study aimed to analyse the frequency of genes encoding virulence factors and to characterize resistance profiles of Staphylococcus aureus isolated from raw milk. In total, 47 and 9 S. aureus isolates were recovered from 150 and 100 raw bovine and ovine milk samples, respectively, in Tunisia. The majority of isolates was resistant to penicillin, and no methicillin-resistant S. aureus was detected. Eighteen and two isolates harboured etd and eta genes respectively. Sixteen enterotoxin-encoding genes were detected (n, %): sed (25, 44·6%), sec (16, 28·6%), sei (16, 28·6%), seh (13, 23·2%), seln (13, 23·2%), sell (10, 17·8%), seg (9, 16%), selu (8, 14·3%), selq (7, 12·5%), selo (7, 12·5%), selm (7, 12·5%), seb (7, 12·5%), sea (6, 10·7%), selk (3, 5·4%), ser (1, 1·8%) and selp (1, 1·8%). Ten isolates carried the tsst1 gene. All isolates carried the haemolysin toxin (hla, hld and hlg). The immune evasion cluster system-type B was predominant (20 isolates) followed by C (3 isolates), A and E (1 isolate each). The occurrence of enterotoxigenic S. aureus in raw milk constitutes a potential risk for human health. SIGNIFICANCE AND IMPACT OF THE STUDY: This paper describes the characteristics of Staphylococcus aureus isolated from raw milk samples from healthy cows and ewes collected from small family farms in Tunisia. Fifty-six strains were analysed by determining their antibiotic susceptibility and genes encoding antibiotic resistance and virulence factors. Methicillin-resistant strains were not detected, and overall low level of antimicrobial resistance was reported. However, our strains harboured several genes encoding virulence factors and 87·5% of them carried at least one gene encoding for enterotoxins showing a high risk of spread of food-borne diseases.

Genetic characterization and antimicrobial resistance of Staphylococcus aureus isolated from bovine milk in Tunisia

Staphylococcus aureus is a major agent of bovine mastitis in dairy herds, causing economic losses in dairy industry worldwide. In addition, milk and milk-products contaminated by Staph. aureus can cause harmful human diseases. The aim of this study was to characterize Staph. aureus strains isolated from dairy farms in Tunisia. Bulk tank milk (n = 32) and individual cow milk (n = 130) samples were collected during the period of 2013-2014. Forty-three Staph. aureus isolates were recovered and typed by spa typing, 16S-23S rRNA intergenic spacer (RS-PCR) and multiplex PCRs for 22 virulence genes. Antimicrobial resistance was also investigated with a disc diffusion test. A selected subsample of 22 strains was additionally genotyped by multilocus sequence typing. Seventeen spa types were recovered, and t2421 (n = 10), t521 (n = 6) and t2112 (n = 5) were the most common. Fourteen different RS-PCR genotypes grouped into 11 clusters were detected in our study, with predominance of the R^VI genotype (n = 24). Eight sequence types were identified and Clonal Complex 97, corresponding to RS-PCR cluster R, was the most common (n = 10), followed by CC1 (n = 4), CC15 (n = 3) and other four accounting for one or two strains. Different combinations of virulence genes were reported, and enterotoxin genes were present in few strains (seh, n = 4; sea, n = 2; sea and seh, n = 2; sec and sel, n = 2). The majority of strains were resistant only to penicillin; only one strain was found to be multiresistant and no methicillin-resistant Staph. aureus was demonstrated. Our study reported the isolation of CC97 from bovine milk in Tunisia for the first time and confirmed the relevance of this lineage in intramammary infection in cows.

SIGNIFICANCE AND IMPACT OF THE STUDY

This paper describes the characteristics of Staphylococcus aureus isolated from bulk tank and individual cow milk in Tunisia. All strains were genotyped by spa typing and RS-PCR, a method based on the amplification of the 16S-23S rRNA intergenic spacer region, and multiplex PCRs for 22 virulence genes. A selected subsample of strains was also genotyped by multilocus sequence typing. All strains were tested for antimicrobial resistance. Our study evidences a predominance of strains belonging to Clonal Complex 97. Methicillin-resistant strains were not detected, and overall low level of antimicrobial resistance was reported.

Nosocomial outbreak of OXA-18-producing Pseudomonas aeruginosa in Tunisia

Following systematic screening for ceftazidime-resistant (CAZ-R) Pseudomonas aeruginosa, 24 isolates producing extended-spectrum beta-lactamase (ESBL) were recovered during a 24-month period at the National Bone Marrow Transplant Centre of Tunisia. These isolates were from seven immunocompromised patients and from environmental swabs. ESBLs inhibited by clavulanic acid were detected by double-disk diffusion tests. Isoelectric focusing revealed that these isolates produced two to four beta-lactamases with pIs of 5.5, 6.1, 6.4, 7.6 or 8.2, and PCR detected the presence of bla(OXA-18), bla(SHV) and bla(TEM) genes in 24, 21 and two isolates, respectively. Pulsed-field gel electrophoresis defined two dominant genotypic groups: group A (16 isolates) and group B (four isolates). Sequencing of PCR products from representative isolates identified the bla(OXA-18) gene and revealed nucleotide sequences belonging to the bla(SHV-1) and bla(TEM-1) genes. Isolates producing OXA-18 belonged to genomic group A and were isolated from four immunocompromised patients in the haematology and graft units, and from two wash-basins in the graft unit. No immunocompromised patient harboured the clonal epidemic strain upon admission. This is the first report of the OXA-18-type ESBL in P. aeruginosa in Tunisia, and the first description of an outbreak caused by an OXA-18-producing strain of P. aeruginosa.

[Characteristics of Enterococcus strains isolated from neutropenic patients at the National Bone-Marrow Transplantation Center of Tunis]

The frequency of digestive colonization of neutropenic patients by Enterococci during the phase of pre-transplant and post-transplant of bone marrow is important indeed as 441 Enterococcus spp strains have been isolated from stool-cultures and other specimens whithin a period of 35 months in 80 patients. A quantitative stool culture was done on appropriate media. Simple bile-esculine agar (BE) and bile esculine-agar additionned with 6 mg/l of vancomycine (BEV) were used for detecting Enterococci. These organisms were taken into account, when then numeration was > 10(3) UFC/g of fecal sample on BE and in all cases on BEV. Species isolated were essentially Enterococcus faecalis (39.4%), Enterococcus faecium (34.4%) and Enterococcus casseliflavus (17%). These strains were characterized by a high frequency of high-level resistance to gentamicin (40.8%). Resistance to amoxicillin concerns 40% of E. faecium strains. Seventeen multiresistant strains of E. faecium isolated from 7 patients (colonized during a long period and receiving a gut decontamination treatment) were the subject of a phenotypic analysis (biotyping, antibiotyping and determination of MICs to beta-lactam, aminoglycosides and glycopeptides). This analysis showed that these strains are distinguishable, endogenic and specific for each patient, the common multiresistance trait resulted from the selective pressure of decontamination treatment used for our patient.