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Limited data are available on the contribution of wildlife to the spread of antibacterial resistance. We determined the prevalence of resistance to antibiotics in Escherichia coli isolates collected from wild animals in 2013 and 2014 and the genetic basis for resistance to third-generation cephalosporin in Guadeloupe. We recovered 52 antibiotic-resistant (AR) E. coli strains from 48 of the 884 (5.4%) wild animals tested (46 iguanas, 181 birds, 289 anoles, and 368 rodents at 163 sampling sites). Rodents had higher rates of carriage (n = 38, 10.3%) than reptiles and birds (2.4% and 1.1%, respectively, p < 0.001). A significant association (p < 0.001) was found between the degree of anthropization and the frequency of AR E. coli carriage for all species. The carriage rate of ciprofloxacin- and cefotaxime-resistant isolates was 0.7% (6/884) and 1.5% (13/884), respectively. Most (65.4%) AR E. coli were multi-drug resistant, and the prevalence of extended-spectrum beta-lactamase (ESBL)-producing E. coli was low (n = 7, 0.8%) in all species. Eight ESBL-producing E. coli were recovered, two genetically unrelated isolates being found in one bird. These isolates and 20 human invasive ESBL E. coli isolates collected in Guadeloupe during the same period were investigated by whole genome sequencing. blaCTX–M–1 was the only ESBL gene shared by three animal classes (humans, n = 2; birds, n = 2; rodents, n = 2). The blaCTX–M–1 gene and most of the antimicrobial resistance genes were present in a large conjugative IncI1 plasmid that was highly similar (>99% nucleotide identity) to ESBL-carrying plasmids found in several countries in Europe and in Australia. Although the prevalence of ESBL-producing E. coli isolates was very low in wild animals, it is of concern that the well-conserved IncI1 plasmid-carrying blaCTX–M–1 is widespread and occurs in various E. coli strains from animals and humans.

Shigella is a major cause of severe diarrhea in children less than the age of 5 years in sub-Saharan Africa. The aim of this study was to describe the (sub-)serotype distribution and antimicrobial susceptibility of Shigella serogroups from Centrafrican patients with diarrhea between 2002 and 2013. We collected 443 Shigella isolates in total. The most common serogroups were Shigella flexneri (N = 243, 54.9%), followed by Shigella sonnei (N = 90, 20.3%) and Shigella dysenteriae (N = 72, 16.3%). The high diversity of (sub-)serotypes of S. flexneri and S. dysenteriae may impede the development of an efficient vaccine. Rates of resistance were high for ampicillin, chloramphenicol, tetracycline, and cotrimoxazole but low for many other antimicrobials, confirming recommendations for the use of third-generation cephalosporins (only one organism resistant) and fluoroquinolones (no resistance). However, the detection of one extended-spectrum beta-lactamase–producing Shigella organism highlights the need for continued monitoring of antimicrobial drug susceptibility.

Significance USA300 is a hypervirulent, community-acquired, multidrug-resistant Staphylococcus aureus clone that started to spread in the United States around 17 years ago. Many studies detected it also in South America, Europe, and the Asia-Pacific region. In this study, we show that USA300 is also circulating in sub-Saharan Africa. Locating the temporal and spatial origin of clonal lineages is important with respect to epidemiology and molecular evolution of pathogens. We show that USA300 evolved from a less virulent and less resistant ancestor circulating in Central Europe around 160 years ago. Constant surveillance of pathogen transmission routes is vital to prevent and control potential outbreaks. Whole genome sequencing proved to be a useful tool for epidemiological surveillance., USA300 is a pandemic clonal lineage of hypervirulent, community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) with specific molecular characteristics. Despite its high clinical relevance, the evolutionary origin of USA300 remained unclear. We used comparative genomics of 224 temporal and spatial diverse S. aureus isolates of multilocus sequence type (ST) 8 to reconstruct the molecular evolution and global dissemination of ST8, including USA300. Analyses of core SNP diversity and accessory genome variations showed that the ancestor of all ST8 S. aureus most likely emerged in Central Europe in the mid-19th century. From here, ST8 was exported to North America in the early 20th century and progressively acquired the USA300 characteristics Panton–Valentine leukocidin (PVL), SCCmec IVa, the arginine catabolic mobile element (ACME), and a specific mutation in capsular polysaccharide gene cap5E. Although the PVL-encoding phage ϕSa2USA was introduced into the ST8 background only once, various SCCmec types were introduced to ST8 at different times and places. Starting from North America, USA300 spread globally, including Africa. African USA300 isolates have aberrant spa-types (t112, t121) and form a monophyletic group within the clade of North American USA300. Large parts of ST8 methicillin-susceptible S. aureus (MSSA) isolated in Africa represent a symplesiomorphic group of ST8 (i.e., a group representing the characteristics of the ancestor), which are rarely found in other world regions. Isolates previously discussed as USA300 ancestors, including USA500 and a “historic” CA-MRSA from Western Australia, were shown to be only distantly related to recent USA300 clones.

Surgical-site infection is the most frequent health care-associated infection in the developing world, with a strikingly higher prevalence than in developed countries We studied the prevalence of resistance to antibiotics in Enterobacteriaceae isolates from surgical-site infections collected in three major tertiary care centres in Bangui, Central African Republic. We also studied the genetic basis for antibiotic resistance and the genetic background of third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae. Between April 2011 and April 2012, 195 patients with nosocomial surgical-site infections were consecutively recruited into the study at five surgical departments in three major tertiary care centres. Of the 165 bacterial isolates collected, most were Enterobacteriaceae (102/165, 61.8%). Of these, 65/102 (63.7%) were 3GC-R, which were characterized for resistance gene determinants and genetic background. The bla CTX-M-15 and aac(6′)-Ib-cr genes were detected in all strains, usually associated with qnr genes (98.5%). Escherichia coli, the most commonly recovered species (33/65, 50.8%), occurred in six different sequence types, including the pandemic B2-O25b-ST131 group (12/33, 36.4%). Resistance transfer was studied in one representative strain of the resistance gene content in each repetitive extragenic palindromic and enterobacterial repetitive intergenic consensus sequence-PCR banding pattern. Plasmids were characterized by PCR-based replicon typing and sub-typing schemes. In most isolates (18/27, 66.7%), bla CTX-M-15 genes were found in incompatibility groups F/F31:A4:B1 and F/F36:A4:B1 conjugative plasmids. Horizontal transfer of both plasmids is probably an important mechanism for the spread of bla CTX-M-15 among Enterobacteriaceae species and hospitals. The presence of sets of antibiotic resistance genes in these two plasmids indicates their capacity for gene rearrangement and their evolution into new variants. Diverse modes are involved in transmission of resistance, plasmid dissemination probably playing a major role.

In January, 2016, a 15-year-old girl with a history only of an ovarian cyst was admitted to hospital in Pointe-a-Pitre, Guadeloupe, with left hemiparesis. 7 days previously she had presented to the emergency department with left arm pain, frontal headaches, and conjunctival hyperaemia, but no fever, signs of meningeal irritation, or sensory or motor defi cits. The day of admission, she developed acute lower back pain, paraesthesia on the left side of her body, and weakness in her left arm. On admission she had slight left-sided weakness and proximal pain of the left arm and leg, exacerbated on movement, but no fever or signs of meningism, and Glasgow Coma Score (GCS) 15. Laboratory analyses were normal except for raised leucocytes (11·5 × 109/L) and polymorphonuclear leucocytes (9·2 × 109/L). Brain MRI was normal. On day 2, she developed dysuria and urinary retention needing catheterisation, but no abnormal urinary frequency or urgency. The left-sided hemiparesis and pain worsened, and we noted loss of temperature sensation below the T2 dermatome on the left and T4 on the right, and bilateral Hoff man signs. Spinal MRI showed lesions of the cervical and thoracic spinal cord. The cervical lesion was enlarged, suggesting oedema (fi gure). Conus medullaris and lumbar roots were normal, suggesting the bladder dysfunction could be linked to spinal damage. Electromyography and cerebrospinal fl uid examination (including isoelectric focusing protein profi le) were normal. We detected high concentrations of Zika virus on specifi c real-time reverse PCR (Eurobio, Les Ulis, France) in serum, urine, and cerebrospinal fl uid on the second day of her admission (9 days after symptom onset). PCR for varicella zoster and herpes simplex viruses, Legionella, and Mycoplasma pneumoniae in her cerebrospinal fl uid were negative. She had no serological signs of acute infection with cytomegalovirus, Epstein-Barr, chikungunya or dengue viruses, syphilis, or Lyme disease; tests for HIV and human T-cell lymphotropic virus (HTLV) were negative; and aquaporin-A antibodies, a marker of neuromyelitis optica, were absent. We started methylprednisolone 1 g daily for 5 days. On the seventh day of admission her neurological condition improved and we could remove the catheter. 1 month after admission she had moderate weakness in both legs but was able to walk unaided. Repeat MRI showed reduced cervical spinal oedema (appendix). The Zika virus epidemic that started in Brazil in May, 2015, spread to 28 countries in February, 2016, including the French Caribbean Islands of Martinique and Guadeloupe. Like dengue, Zika is an arthropod-borne virus of the Flaviviridae family transmitted by Aedes mosquitoes. Until recently, Zika was thought to cause benign infections in humans. The presence of Zika virus in the cerebrospinal fl uid of our patient with acute myelitis suggests that this virus might be neurotropic. In addition to the usual clinical picture of myelitis she had severe pain. Absence of intrathecal immunoglobulins and normal brain MRI excluded acute disseminated encephalomyelitis. The neurotropism of fl aviviruses such as dengue, Japanese encephalitis, and West Nile viruses, which might be responsible for invasive encephalitis and transverse or extensive myelitis, is well documented. West Nile virus might also aff ect lumbosacral nerve roots in addition to the spinal cord, and retrograde axonal transport from infected peripheral nerves has been shown. Zika virus infection should be considered in patients with acute myelitis living in or travelling from endemic areas, and further study should clarify the spectrum and incidence of neurological associations.